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/7922901/working' mkdir: created directory `/scratch/stefan/7922901/working/protonate' Storing results in /scratch/stefan/7922901/finished Working in /scratch/stefan/7922901/working /scratch/stefan/7922901/working /scratch/stefan/7922901 /scratch/stefan/7922901/working/protonate /scratch/stefan/7922901/working /scratch/stefan/7922901 Precomputing protomers for all compounds (pH: 7.4) ph 7.4: 1069 protomers created Coalesing and merging protomers 1034 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1051 protomers after new stereo-center expansion /scratch/stefan/7922901/working /scratch/stefan/7922901 Bulk generating 3D conformations all protomers in /scratch/stefan/7922901/working/3D mkdir: created directory `/scratch/stefan/7922901/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7922901/working/protonate/xaaaaaq-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' 1052 3D conformations generated for 1000 compounds Building REAL250005053893 mkdir: created directory `/scratch/stefan/7922901/working/building' mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053893' /scratch/stefan/7922901/working/building/REAL250005053893 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053893 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053893/0 /scratch/stefan/7922901/working/building/REAL250005053893 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1 `/scratch/stefan/7922901/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053893.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053893 none CCOCCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 176, 171, 153, 74, 74, 74, 60, 42, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 177, 177, 174, 174, 154, 154, 74, 60, 60, 42, 42, 18, 18, 18, 1] 178 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: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053893 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053893 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `/scratch/stefan/7922901/finished' Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053893/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053893 Building REAL250005053894 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053894' /scratch/stefan/7922901/working/building/REAL250005053894 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053894 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053894/0 /scratch/stefan/7922901/working/building/REAL250005053894 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/2 `/scratch/stefan/7922901/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)COCC1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053894.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053894 none CN(CCNC(=O)COCC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 8, 14, 20, 23, 23, 23, 59, 95, 137, 201, 201, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 20, 20, 23, 59, 59, 137, 137, 201, 201, 201, 201, 201, 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: 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: REAL250005053894 none CN(CCNC(=O)COCC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 155, 131, 91, 91, 58, 91, 25, 9, 1, 1, 1, 1, 169, 201, 201, 201, 201, 201, 201, 201, 169, 169, 169, 155, 155, 131, 131, 91, 58, 58, 9, 9, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 835 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053894 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053894 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053894/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053894 Building REAL250005053895 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053895' /scratch/stefan/7922901/working/building/REAL250005053895 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053895 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053895/0 /scratch/stefan/7922901/working/building/REAL250005053895 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/3 `/scratch/stefan/7922901/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1CCCO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053895.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053895 none CN(CCNC(=O)CC1CCCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 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: [20, 7, 20, 39, 44, 83, 83, 83, 182, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 39, 39, 44, 44, 83, 182, 182, 201, 201, 201, 201, 201, 201, 201, 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: 781 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053895 none CN(CCNC(=O)CC1CCCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 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: [159, 131, 93, 31, 31, 9, 31, 1, 1, 1, 1, 1, 1, 159, 195, 195, 201, 201, 201, 201, 201, 159, 159, 159, 131, 131, 93, 93, 31, 9, 9, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38]) total number of confs: 800 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053895 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053895 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053895/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053895 Building REAL250005053896 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053896' /scratch/stefan/7922901/working/building/REAL250005053896 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053896 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053896/0 /scratch/stefan/7922901/working/building/REAL250005053896 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/4 `/scratch/stefan/7922901/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CNN=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053896.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053896 none CN(CCNC(=O)C1=CNN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.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', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 24, 48, 58, 79, 79, 79, 79, 79, 79, 79, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 48, 48, 58, 58, 79, 79, 79, 79, 1] 79 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: 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: REAL250005053896 none CN(CCNC(=O)C1=CNN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.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', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [43, 25, 15, 3, 3, 1, 3, 1, 1, 1, 1, 1, 43, 73, 73, 79, 79, 79, 79, 79, 43, 43, 43, 25, 25, 15, 15, 3, 1, 1, 1, 79] 79 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053896 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053896 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053896/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053896 Building REAL250005053897 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053897' /scratch/stefan/7922901/working/building/REAL250005053897 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053897 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053897/0 /scratch/stefan/7922901/working/building/REAL250005053897 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/5 `/scratch/stefan/7922901/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053897.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053897 none COCCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 175, 89, 89, 89, 65, 45, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 189, 189, 185, 185, 177, 177, 89, 65, 65, 45, 45, 18, 18, 18, 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: 1007 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053897 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053897 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053897/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053897 Building REAL250005053898 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053898' /scratch/stefan/7922901/working/building/REAL250005053898 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053898 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053898/0 /scratch/stefan/7922901/working/building/REAL250005053898 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/6 `/scratch/stefan/7922901/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053898.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053898 none CCOC1CC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 139, 139, 139, 61, 61, 61, 44, 38, 15, 7, 15, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 139, 139, 139, 139, 61, 44, 44, 38, 38, 15, 15, 15, 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: 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: REAL250005053898 none CCOC1CC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 11, 11, 11, 39, 61, 82, 82, 120, 120, 139, 139, 139, 139, 139, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 39, 39, 61, 61, 82, 82, 82, 139] 201 rigid atoms, others: [2, 3, 4, 5, 6, 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, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 557 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053898 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053898 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053898/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053898 Building REAL250005053899 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053899' /scratch/stefan/7922901/working/building/REAL250005053899 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053899 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053899/0 /scratch/stefan/7922901/working/building/REAL250005053899 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/7 `/scratch/stefan/7922901/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NSN=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053899.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053899 none CN(CCNC(=O)C1=NSN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 14, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 6, 18, 25, 25, 31, 31, 31, 53, 53, 53, 53, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 25, 25, 25, 25, 31, 53, 1] 53 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: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053899 none CN(CCNC(=O)C1=NSN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 14, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 31, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 37, 53, 53, 53, 53, 53, 53, 53, 37, 37, 37, 31, 31, 25, 25, 7, 1, 53] 53 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053899 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053899 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053899/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053899 Building REAL250005053900 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053900' /scratch/stefan/7922901/working/building/REAL250005053900 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053900 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053900/0 /scratch/stefan/7922901/working/building/REAL250005053900 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/8 `/scratch/stefan/7922901/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CN=NS1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053900.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053900 none CN(CCNC(=O)C1=CN=NS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 6, 16, 38, 45, 72, 72, 72, 117, 117, 117, 117, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 38, 38, 45, 45, 72, 117, 1] 117 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: 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: REAL250005053900 none CN(CCNC(=O)C1=CN=NS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [66, 44, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 66, 115, 115, 117, 117, 117, 117, 117, 66, 66, 66, 44, 44, 28, 28, 9, 1, 117] 117 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29]) total number of confs: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053900 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053900 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053900/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053900 Building REAL250005053901 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053901' /scratch/stefan/7922901/working/building/REAL250005053901 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053901 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053901/0 /scratch/stefan/7922901/working/building/REAL250005053901 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/9 `/scratch/stefan/7922901/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NOC=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053901.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053901 none CN(CCNC(=O)C1=NOC=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', '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: [5, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [16, 6, 16, 23, 23, 31, 31, 31, 45, 45, 45, 45, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 23, 23, 23, 23, 31, 45, 45, 1] 45 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: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053901 none CN(CCNC(=O)C1=NOC=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', '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: [5, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 29, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 33, 45, 45, 45, 45, 45, 45, 45, 33, 33, 33, 29, 29, 19, 19, 7, 1, 1, 45] 45 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053901 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053901 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053901/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053901 Building REAL250005053902 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053902' /scratch/stefan/7922901/working/building/REAL250005053902 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053902 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053902/0 /scratch/stefan/7922901/working/building/REAL250005053902 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/10 `/scratch/stefan/7922901/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005053902.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053902 none CC(=CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 77, 107, 131, 131, 182, 182, 201, 201, 201, 201, 201, 1, 1, 1, 7, 7, 7, 7, 27, 77, 77, 107, 107, 131, 131, 131, 201, 1, 1, 1, 1, 1] 201 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: 756 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053902 none CC(=CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 55, 55, 55, 42, 33, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 119, 201, 201, 119, 119, 119, 119, 55, 42, 42, 33, 33, 15, 15, 15, 1, 201, 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, 38]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053902 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053902 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053902/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053902 Building REAL250005053903 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053903' /scratch/stefan/7922901/working/building/REAL250005053903 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053903 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053903/0 /scratch/stefan/7922901/working/building/REAL250005053903 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/11 `/scratch/stefan/7922901/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005053903.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053903 none CC1=NNC(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 111, 111, 111, 77, 59, 22, 10, 22, 1, 10, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 111, 77, 77, 59, 59, 22, 22, 22, 1, 120] 120 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: 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: REAL250005053903 none CC1=NNC(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 20, 32, 56, 56, 106, 106, 120, 120, 120, 120, 120, 1, 2, 2, 2, 1, 7, 20, 20, 32, 32, 56, 56, 56, 120, 1] 120 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: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053903 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053903 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053903/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053903 Building REAL250005053904 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053904' /scratch/stefan/7922901/working/building/REAL250005053904 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053904 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053904/0 /scratch/stefan/7922901/working/building/REAL250005053904 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/12 `/scratch/stefan/7922901/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CN=CS1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053904.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053904 none CN(CCNC(=O)C1=CN=CS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 10, 26, 53, 67, 101, 101, 101, 165, 165, 165, 165, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 53, 53, 67, 67, 101, 165, 165, 1] 165 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: 505 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053904 none CN(CCNC(=O)C1=CN=CS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [97, 63, 41, 10, 10, 1, 10, 1, 1, 1, 1, 1, 97, 157, 157, 165, 165, 165, 165, 165, 97, 97, 97, 63, 63, 40, 40, 10, 1, 1, 165] 165 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053904 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053904 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053904/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053904 Building REAL250005053905 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053905' /scratch/stefan/7922901/working/building/REAL250005053905 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053905 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053905/0 /scratch/stefan/7922901/working/building/REAL250005053905 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/13 `/scratch/stefan/7922901/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053905.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053905 none CCC=C(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 199, 77, 199, 77, 77, 51, 40, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 199, 199, 199, 77, 51, 51, 40, 40, 17, 17, 17, 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: 632 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053905 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053905 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053905/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053905 Building REAL250005053906 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053906' /scratch/stefan/7922901/working/building/REAL250005053906 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053906 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053906/0 /scratch/stefan/7922901/working/building/REAL250005053906 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/14 `/scratch/stefan/7922901/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)N=CO1) `REAL250005053906.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053906 none CC1=C(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 201, 180, 180, 180, 95, 59, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 180, 95, 95, 59, 59, 21, 21, 21, 1, 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]) total number of confs: 699 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: REAL250005053906 none CC1=C(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 7, 7, 7, 31, 53, 93, 93, 178, 178, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 7, 31, 31, 53, 53, 93, 93, 93, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 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: 675 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053906 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053906 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053906/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053906 Building REAL250005053907 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053907' /scratch/stefan/7922901/working/building/REAL250005053907 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053907 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053907/0 /scratch/stefan/7922901/working/building/REAL250005053907 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/15 `/scratch/stefan/7922901/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(CC)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053907.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053907 none CCOC(CC)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 186, 126, 186, 189, 126, 126, 66, 43, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 187, 187, 187, 187, 187, 186, 201, 201, 201, 201, 201, 126, 66, 66, 43, 43, 16, 16, 16, 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.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053907 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053907 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053907/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053907 Building REAL250005053908 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053908' /scratch/stefan/7922901/working/building/REAL250005053908 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053908 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053908/0 /scratch/stefan/7922901/working/building/REAL250005053908 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/16 `/scratch/stefan/7922901/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC(F)(F)F)C(=O)C1=CC(=O)[N-]O1) `REAL250005053908.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053908 none CN(CCNC(=O)CC(F)(F)F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 5, 15, 15, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 49, 61, 101, 101, 101, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 49, 49, 61, 61, 101, 201, 201, 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: 833 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053908 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053908 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053908/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053908 Building REAL250005053909 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053909' /scratch/stefan/7922901/working/building/REAL250005053909 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053909 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053909/0 /scratch/stefan/7922901/working/building/REAL250005053909 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/17 `/scratch/stefan/7922901/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053909.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053909 none COC(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 154, 201, 154, 154, 86, 56, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 154, 86, 86, 56, 56, 20, 20, 20, 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: 820 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053909 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053909 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053909/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053909 Building REAL250005053910 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053910' /scratch/stefan/7922901/working/building/REAL250005053910 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053910 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053910/0 /scratch/stefan/7922901/working/building/REAL250005053910 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/18 `/scratch/stefan/7922901/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053910.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053910 none CC(C)OCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 133, 201, 112, 103, 103, 103, 70, 48, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 112, 112, 103, 70, 70, 48, 48, 16, 16, 16, 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: 900 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053910 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053910 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053910/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053910 Building REAL250005053911 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053911' /scratch/stefan/7922901/working/building/REAL250005053911 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053911 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053911/0 /scratch/stefan/7922901/working/building/REAL250005053911 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/19 `/scratch/stefan/7922901/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053911.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053911 none CCCOCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 144, 124, 86, 55, 55, 55, 45, 41, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 144, 144, 86, 86, 55, 45, 45, 41, 41, 16, 16, 16, 1] 184 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: 801 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053911 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053911 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053911/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053911 Building REAL250005053912 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053912' /scratch/stefan/7922901/working/building/REAL250005053912 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053912 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053912/0 /scratch/stefan/7922901/working/building/REAL250005053912 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/20 `/scratch/stefan/7922901/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCOC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053912.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053912 none CN(CCNC(=O)C1CCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 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, 25, 52, 66, 109, 109, 109, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 25, 52, 52, 66, 66, 109, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005053912 none CN(CCNC(=O)C1CCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 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: [121, 74, 41, 8, 8, 1, 8, 1, 1, 1, 1, 1, 121, 191, 191, 201, 201, 201, 201, 201, 121, 121, 121, 74, 74, 41, 41, 8, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35]) total number of confs: 761 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053912 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053912 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053912/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053912 Building REAL250005053913 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053913' /scratch/stefan/7922901/working/building/REAL250005053913 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053913 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053913/0 /scratch/stefan/7922901/working/building/REAL250005053913 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/21 `/scratch/stefan/7922901/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC=NN1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053913.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053913 none CN(CCNC(=O)C1=CC=NN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 10, 28, 57, 75, 123, 123, 123, 147, 147, 147, 147, 147, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 57, 57, 75, 75, 123, 147, 147, 147, 147, 147, 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: 485 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: REAL250005053913 none CN(CCNC(=O)C1=CC=NN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [81, 61, 38, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 81, 134, 134, 147, 147, 147, 147, 147, 81, 81, 81, 61, 61, 38, 38, 10, 1, 1, 2, 2, 2, 147] 147 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 528 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053913 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053913 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053913/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053913 Building REAL250005053914 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053914' /scratch/stefan/7922901/working/building/REAL250005053914 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053914 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053914/0 /scratch/stefan/7922901/working/building/REAL250005053914 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/22 `/scratch/stefan/7922901/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053914.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053914 none CCC(OC)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 158, 115, 158, 166, 115, 115, 67, 48, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 158, 166, 166, 166, 115, 67, 67, 48, 48, 20, 20, 20, 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: 953 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053914 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053914 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053914/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053914 Building REAL250005053915 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053915' /scratch/stefan/7922901/working/building/REAL250005053915 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053915 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053915/0 /scratch/stefan/7922901/working/building/REAL250005053915 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/23 `/scratch/stefan/7922901/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053915.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053915 none COCCCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 157, 147, 139, 52, 52, 52, 42, 35, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 196, 196, 196, 196, 196, 157, 157, 157, 157, 143, 143, 52, 42, 42, 35, 35, 16, 16, 16, 1] 196 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 947 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053915 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053915 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053915/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053915 Building REAL250005053916 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053916' /scratch/stefan/7922901/working/building/REAL250005053916 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053916 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053916/0 /scratch/stefan/7922901/working/building/REAL250005053916 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/24 `/scratch/stefan/7922901/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053916.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053916 none CCCC(C)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 159, 195, 53, 53, 53, 50, 40, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 159, 159, 53, 50, 50, 40, 40, 17, 17, 17, 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: 885 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053916 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053916 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053916/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053916 Building REAL250005053917 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053917' /scratch/stefan/7922901/working/building/REAL250005053917 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053917 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053917/0 /scratch/stefan/7922901/working/building/REAL250005053917 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/25 `/scratch/stefan/7922901/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053917.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053917 none COC(C)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 188, 141, 141, 141, 84, 59, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 188, 188, 188, 188, 141, 84, 84, 59, 59, 17, 17, 17, 1] 188 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: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053917 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053917 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053917/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053917 Building REAL250005053918 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053918' /scratch/stefan/7922901/working/building/REAL250005053918 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053918 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053918/0 /scratch/stefan/7922901/working/building/REAL250005053918 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/26 `/scratch/stefan/7922901/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053918.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053918 none C=CCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 139, 139, 51, 51, 51, 39, 35, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 141, 141, 51, 39, 39, 35, 35, 18, 18, 18, 1] 141 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: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053918 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053918 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053918/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053918 Building REAL250005053919 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053919' /scratch/stefan/7922901/working/building/REAL250005053919 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053919 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053919/0 /scratch/stefan/7922901/working/building/REAL250005053919 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/27 `/scratch/stefan/7922901/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=COCCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053919.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053919 none CN(CCNC(=O)C1=COCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 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, 10, 25, 50, 57, 99, 99, 99, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 50, 50, 57, 57, 99, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005053919 none CN(CCNC(=O)C1=COCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 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: [130, 86, 57, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 130, 195, 195, 201, 201, 201, 201, 201, 130, 130, 130, 86, 86, 57, 57, 12, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 765 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053919 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053919 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053919/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053919 Building REAL250005053920 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053920' /scratch/stefan/7922901/working/building/REAL250005053920 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053920 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053920/0 /scratch/stefan/7922901/working/building/REAL250005053920 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/28 `/scratch/stefan/7922901/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCCOC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053920.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053920 none CN(CCNC(=O)C1CCCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 3, 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, 26, 53, 64, 106, 106, 106, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 53, 53, 64, 64, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005053920 none CN(CCNC(=O)C1CCCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 3, 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: [129, 87, 53, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 129, 191, 191, 201, 201, 201, 201, 201, 129, 129, 129, 87, 87, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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/7922901/working/building/REAL250005053920 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053920 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053920/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053920 Building REAL250005053921 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053921' /scratch/stefan/7922901/working/building/REAL250005053921 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053921 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053921/0 /scratch/stefan/7922901/working/building/REAL250005053921 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/29 `/scratch/stefan/7922901/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053921.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053921 none CCOCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 179, 110, 110, 110, 60, 46, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 179, 179, 179, 179, 179, 110, 60, 60, 46, 46, 16, 16, 16, 1] 179 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: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053921 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053921 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053921/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053921 Building REAL250005053922 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053922' /scratch/stefan/7922901/working/building/REAL250005053922 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053922 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053922/0 /scratch/stefan/7922901/working/building/REAL250005053922 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/30 `/scratch/stefan/7922901/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CSC=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053922.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053922 none CN(CCNC(=O)C1=CSC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 6, 20, 31, 33, 53, 53, 53, 75, 75, 75, 75, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 31, 31, 33, 33, 53, 75, 75, 1] 75 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: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053922 none CN(CCNC(=O)C1=CSC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [61, 51, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 61, 75, 75, 75, 75, 75, 75, 75, 61, 61, 61, 51, 51, 37, 37, 11, 1, 1, 75] 75 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053922 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053922 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053922/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053922 Building REAL250005053923 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053923' /scratch/stefan/7922901/working/building/REAL250005053923 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053923 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053923/0 /scratch/stefan/7922901/working/building/REAL250005053923 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/31 `/scratch/stefan/7922901/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053923.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053923 none COCC(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 124, 171, 124, 124, 76, 56, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 171, 171, 171, 171, 171, 124, 76, 76, 56, 56, 18, 18, 18, 1] 171 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: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053923 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053923 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053923/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053923 Building REAL250005053924 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053924' /scratch/stefan/7922901/working/building/REAL250005053924 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053924 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053924/0 /scratch/stefan/7922901/working/building/REAL250005053924 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/32 `/scratch/stefan/7922901/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053924.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053924 none C=CCOCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 93, 79, 41, 41, 41, 39, 31, 17, 8, 17, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 79, 79, 41, 39, 39, 31, 31, 17, 17, 17, 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: 855 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053924 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053924 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053924/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053924 Building REAL250005053925 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053925' /scratch/stefan/7922901/working/building/REAL250005053925 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053925 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053925/0 /scratch/stefan/7922901/working/building/REAL250005053925 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/33 `/scratch/stefan/7922901/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=COC=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053925.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053925 none CN(CCNC(=O)C1=COC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [18, 6, 18, 29, 29, 41, 41, 41, 65, 65, 65, 65, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 29, 29, 29, 29, 41, 65, 65, 1] 65 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: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053925 none CN(CCNC(=O)C1=COC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [45, 37, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 45, 65, 65, 65, 65, 65, 65, 65, 45, 45, 45, 37, 37, 25, 25, 7, 1, 1, 65] 65 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/7922901/working/building/REAL250005053925 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053925 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053925/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053925 Building REAL250005053926 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053926' /scratch/stefan/7922901/working/building/REAL250005053926 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053926 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053926/0 /scratch/stefan/7922901/working/building/REAL250005053926 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/34 `/scratch/stefan/7922901/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1CCC(=O)N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053926.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053926 none CN(CCNC(=O)[C@H]1CCC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 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 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [22, 9, 22, 30, 30, 59, 59, 59, 93, 93, 93, 93, 93, 93, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 22, 30, 30, 30, 30, 59, 93, 93, 93, 93, 93, 1] 93 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: 299 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: REAL250005053926 none CN(CCNC(=O)[C@H]1CCC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 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 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [71, 63, 45, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 71, 91, 91, 93, 93, 93, 93, 93, 71, 71, 71, 63, 63, 45, 45, 11, 1, 1, 1, 1, 1, 93] 93 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 369 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053926 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053926 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053926/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053926 Building REAL250005053927 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053927' /scratch/stefan/7922901/working/building/REAL250005053927 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053927 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053927/0 /scratch/stefan/7922901/working/building/REAL250005053927 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/35 `/scratch/stefan/7922901/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)N1) `REAL250005053927.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053927 none CC1=NC=C(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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 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, 140, 140, 140, 94, 72, 30, 12, 30, 1, 12, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 140, 94, 94, 72, 72, 30, 30, 30, 1, 154] 154 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: 556 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053927 none CC1=NC=C(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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 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, 6, 6, 6, 30, 49, 74, 74, 134, 134, 154, 154, 154, 154, 154, 1, 2, 2, 2, 1, 6, 30, 30, 49, 49, 74, 74, 74, 154, 1] 154 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: 526 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053927 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053927 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053927/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053927 Building REAL250005053928 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053928' /scratch/stefan/7922901/working/building/REAL250005053928 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005053928 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053928/0 /scratch/stefan/7922901/working/building/REAL250005053928 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/36 `/scratch/stefan/7922901/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCC[N@@H+]1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053928.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053928 none CN(CCNC(=O)C1CCC[N@@H+]1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 8, 11, 11, 11, 12, 12, 12, 12, 12, 12, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 12 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: 35 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: REAL250005053928 none CN(CCNC(=O)C1CCC[N@@H+]1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12] 12 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40]) total number of confs: 56 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053928 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005053928/1 /scratch/stefan/7922901/working/building/REAL250005053928 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/37 `/scratch/stefan/7922901/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCC[N@H+]1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053928.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005053928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053928 none CN(CCNC(=O)C1CCC[N@H+]1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 8, 11, 11, 11, 12, 12, 12, 12, 12, 12, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 12 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: 35 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: REAL250005053928 none CN(CCNC(=O)C1CCC[N@H+]1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12] 12 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40]) total number of confs: 56 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053928 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `2' /scratch/stefan/7922901/working/building/REAL250005053928/2 /scratch/stefan/7922901/working/building/REAL250005053928 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 2 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/38 `/scratch/stefan/7922901/working/3D/38' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCCN1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053928.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005053928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053928/2/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: REAL250005053928 none CN(CCNC(=O)C1CCCN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 9, 21, 30, 30, 56, 56, 56, 92, 92, 92, 92, 92, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 30, 30, 30, 30, 56, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 1] 92 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: 309 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053928 none CN(CCNC(=O)C1CCCN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 10, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [77, 63, 43, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 77, 92, 92, 92, 92, 92, 92, 92, 77, 77, 77, 63, 63, 43, 43, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 92] 92 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39]) total number of confs: 380 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053928 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053928 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053928/0.* 1: /scratch/stefan/7922901/working/building/REAL250005053928/1.* 2: /scratch/stefan/7922901/working/building/REAL250005053928/2.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053928 Building REAL250005053929 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053929' /scratch/stefan/7922901/working/building/REAL250005053929 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053929 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053929/0 /scratch/stefan/7922901/working/building/REAL250005053929 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/39 `/scratch/stefan/7922901/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053929.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053929 none CCC(=O)NCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 116, 116, 116, 110, 52, 52, 52, 47, 39, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 116, 110, 110, 52, 47, 47, 39, 39, 15, 15, 15, 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: 1039 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053929 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053929 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053929/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053929 Building REAL250005053930 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053930' /scratch/stefan/7922901/working/building/REAL250005053930 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053930 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053930/0 /scratch/stefan/7922901/working/building/REAL250005053930 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/40 `/scratch/stefan/7922901/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C=CC(C)(C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053930.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053930 none CN(CCNC(=O)C=CC(C)(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 22, 48, 60, 101, 101, 101, 193, 193, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 48, 48, 60, 60, 101, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 711 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053930 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053930 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053930/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053930 Building REAL250005053931 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053931' /scratch/stefan/7922901/working/building/REAL250005053931 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053931 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053931/0 /scratch/stefan/7922901/working/building/REAL250005053931 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/41 `/scratch/stefan/7922901/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053931.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053931 none CCCC(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 156, 73, 156, 73, 73, 53, 43, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 171, 171, 171, 156, 156, 156, 156, 73, 53, 53, 43, 43, 16, 16, 16, 1] 171 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: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053931 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053931 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053931/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053931 Building REAL250005053932 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053932' /scratch/stefan/7922901/working/building/REAL250005053932 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053932 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053932/0 /scratch/stefan/7922901/working/building/REAL250005053932 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/42 `/scratch/stefan/7922901/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCC1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053932.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053932 none CN(CCNC(=O)CCC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 25, 27, 49, 49, 49, 148, 158, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 25, 25, 27, 27, 49, 148, 148, 162, 162, 201, 201, 201, 201, 201, 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: 815 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053932 none CN(CCNC(=O)CCC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 164, 122, 34, 34, 7, 34, 3, 1, 1, 1, 1, 188, 199, 199, 201, 201, 201, 201, 201, 187, 188, 188, 164, 164, 122, 122, 34, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11] 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, 28, 29, 30, 31, 37]) total number of confs: 833 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053932 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053932 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053932/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053932 Building REAL250005053933 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053933' /scratch/stefan/7922901/working/building/REAL250005053933 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053933 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053933/0 /scratch/stefan/7922901/working/building/REAL250005053933 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/43 `/scratch/stefan/7922901/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053933.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053933 none CCCCOCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 113, 99, 50, 50, 50, 26, 22, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 117, 117, 99, 99, 50, 26, 26, 22, 22, 11, 11, 11, 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: 890 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053933 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053933 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053933/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053933 Building REAL250005053934 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053934' /scratch/stefan/7922901/working/building/REAL250005053934 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053934 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053934/0 /scratch/stefan/7922901/working/building/REAL250005053934 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/44 `/scratch/stefan/7922901/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1=NOC=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053934.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053934 none CN(CCNC(=O)CC1=NOC=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 8, 12, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 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: [16, 6, 16, 23, 23, 53, 53, 53, 161, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 23, 23, 23, 23, 53, 161, 161, 201, 201, 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: 663 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053934 none CN(CCNC(=O)CC1=NOC=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 8, 12, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 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: [161, 137, 108, 27, 27, 5, 27, 1, 1, 1, 1, 1, 1, 161, 201, 201, 201, 201, 201, 201, 201, 161, 161, 161, 137, 137, 108, 108, 27, 5, 5, 1, 1, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 797 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053934 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053934 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053934/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053934 Building REAL250005053935 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053935' /scratch/stefan/7922901/working/building/REAL250005053935 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053935 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053935/0 /scratch/stefan/7922901/working/building/REAL250005053935 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/45 `/scratch/stefan/7922901/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1CCOC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053935.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053935 none CN(CCNC(=O)CC1CCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 3, 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: [19, 6, 19, 34, 38, 60, 60, 60, 176, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 34, 34, 38, 38, 60, 176, 176, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005053935 none CN(CCNC(=O)CC1CCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 3, 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: [172, 144, 106, 29, 29, 6, 29, 1, 1, 1, 1, 1, 1, 172, 196, 196, 201, 201, 201, 201, 201, 172, 172, 172, 144, 144, 106, 106, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38]) total number of confs: 804 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053935 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053935 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053935/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053935 Building REAL250005053936 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053936' /scratch/stefan/7922901/working/building/REAL250005053936 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053936 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053936/0 /scratch/stefan/7922901/working/building/REAL250005053936 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/46 `/scratch/stefan/7922901/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC=CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053936.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053936 none CN(CCNC(=O)C1CC=CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 23, 50, 62, 111, 111, 111, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 23, 23, 23, 50, 50, 62, 62, 111, 201, 201, 201, 201, 201, 201, 201, 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: 677 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053936 none CN(CCNC(=O)C1CC=CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 74, 45, 9, 9, 1, 9, 1, 1, 1, 1, 1, 116, 194, 194, 201, 201, 201, 201, 201, 116, 116, 116, 74, 74, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053936 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053936 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053936/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053936 Building REAL250005053937 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053937' /scratch/stefan/7922901/working/building/REAL250005053937 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053937 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053937/0 /scratch/stefan/7922901/working/building/REAL250005053937 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/47 `/scratch/stefan/7922901/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1=NNC=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053937.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053937 none CN(CCNC(=O)CC1=NNC=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 15, 25, 27, 53, 53, 53, 147, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 25, 25, 27, 27, 53, 147, 147, 201, 201, 201, 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: 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: REAL250005053937 none CN(CCNC(=O)CC1=NNC=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 151, 103, 31, 31, 9, 31, 1, 1, 1, 1, 1, 1, 176, 200, 200, 201, 201, 201, 201, 201, 176, 176, 176, 151, 151, 103, 103, 31, 9, 9, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 842 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053937 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053937 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053937/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053937 Building REAL250005053938 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053938' /scratch/stefan/7922901/working/building/REAL250005053938 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053938 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053938/0 /scratch/stefan/7922901/working/building/REAL250005053938 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/48 `/scratch/stefan/7922901/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053938.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053938 none CN(CCNC(=O)CC1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 35, 39, 69, 69, 69, 152, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 35, 35, 39, 39, 69, 152, 152, 201, 201, 201, 201, 201, 201, 201, 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: 845 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053938 none CN(CCNC(=O)CC1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 133, 97, 33, 33, 6, 33, 1, 1, 1, 1, 1, 175, 200, 200, 201, 201, 201, 201, 201, 175, 175, 175, 133, 132, 97, 97, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37]) total number of confs: 813 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053938 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053938 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053938/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053938 Building REAL250005053939 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053939' /scratch/stefan/7922901/working/building/REAL250005053939 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053939 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053939/0 /scratch/stefan/7922901/working/building/REAL250005053939 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/49 `/scratch/stefan/7922901/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)OC=N1) `REAL250005053939.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053939 none CC1=C(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 201, 162, 162, 162, 89, 55, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 162, 89, 89, 55, 55, 22, 22, 22, 1, 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]) total number of confs: 681 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: REAL250005053939 none CC1=C(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 7, 7, 7, 32, 57, 98, 98, 189, 189, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 8, 31, 31, 57, 57, 98, 98, 98, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 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: 715 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053939 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053939 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053939/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053939 Building REAL250005053940 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053940' /scratch/stefan/7922901/working/building/REAL250005053940 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053940 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053940/0 /scratch/stefan/7922901/working/building/REAL250005053940 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/50 `/scratch/stefan/7922901/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005053940.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053940 none CC(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 47, 78, 101, 101, 161, 161, 201, 201, 201, 201, 201, 1, 1, 1, 3, 3, 3, 3, 16, 47, 47, 78, 78, 101, 101, 101, 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: 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: REAL250005053940 none CC(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 65, 47, 20, 10, 20, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 92, 65, 65, 47, 47, 20, 20, 20, 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: 849 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053940 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053940 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053940/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053940 Building REAL250005053941 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053941' /scratch/stefan/7922901/working/building/REAL250005053941 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053941 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053941/0 /scratch/stefan/7922901/working/building/REAL250005053941 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/51 `/scratch/stefan/7922901/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1C2CCCC21)C(=O)C1=CC(=O)[N-]O1) `REAL250005053941.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053941 none CN(CCNC(=O)C1C2CCCC21)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 29, 73, 97, 159, 159, 159, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 73, 73, 97, 97, 159, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005053941 none CN(CCNC(=O)C1C2CCCC21)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 79, 182, 182, 201, 201, 201, 201, 201, 79, 79, 79, 44, 44, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38]) total number of confs: 636 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053941 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053941 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053941/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053941 Building REAL250005053942 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053942' /scratch/stefan/7922901/working/building/REAL250005053942 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053942 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053942/0 /scratch/stefan/7922901/working/building/REAL250005053942 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/52 `/scratch/stefan/7922901/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCC1CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053942.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053942 none CN(CCNC(=O)CCC1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 20, 22, 27, 27, 27, 104, 120, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 20, 20, 22, 22, 27, 104, 104, 142, 142, 201, 201, 201, 201, 201, 201, 201, 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: 919 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053942 none CN(CCNC(=O)CCC1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 153, 112, 50, 50, 12, 50, 6, 1, 1, 1, 1, 1, 173, 194, 194, 201, 201, 201, 201, 201, 173, 173, 173, 153, 153, 112, 112, 50, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40]) total number of confs: 861 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053942 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053942 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053942/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053942 Building REAL250005053943 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053943' /scratch/stefan/7922901/working/building/REAL250005053943 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053943 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053943/0 /scratch/stefan/7922901/working/building/REAL250005053943 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/53 `/scratch/stefan/7922901/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053943.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053943 none CC=C(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 201, 127, 127, 83, 65, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 127, 83, 83, 65, 65, 22, 22, 22, 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: 727 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053943 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053943 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053943/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053943 Building REAL250005053944 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053944' /scratch/stefan/7922901/working/building/REAL250005053944 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053944 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053944/0 /scratch/stefan/7922901/working/building/REAL250005053944 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/54 `/scratch/stefan/7922901/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005053944.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053944 none CC1CC(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 105, 105, 105, 66, 52, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 105, 66, 66, 52, 52, 20, 20, 20, 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: 694 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: REAL250005053944 none CC1CC(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 53, 86, 134, 134, 192, 192, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 12, 53, 53, 86, 86, 134, 134, 134, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 19, 23, 24, 25, 26, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 768 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053944 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053944 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053944/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053944 Building REAL250005053945 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053945' /scratch/stefan/7922901/working/building/REAL250005053945 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053945 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053945/0 /scratch/stefan/7922901/working/building/REAL250005053945 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/55 `/scratch/stefan/7922901/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C=C1CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053945.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053945 none CN(CCNC(=O)C=C1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 54, 69, 112, 112, 112, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 54, 54, 69, 69, 112, 201, 201, 201, 201, 201, 201, 201, 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: 701 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: REAL250005053945 none CN(CCNC(=O)C=C1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 88, 51, 10, 10, 1, 10, 1, 1, 1, 1, 1, 124, 194, 194, 201, 201, 201, 201, 201, 124, 124, 124, 88, 88, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35]) total number of confs: 775 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053945 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053945 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053945/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053945 Building REAL250005053946 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053946' /scratch/stefan/7922901/working/building/REAL250005053946 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053946 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053946/0 /scratch/stefan/7922901/working/building/REAL250005053946 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/56 `/scratch/stefan/7922901/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)CC) `REAL250005053946.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053946 none CCC(=CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 109, 109, 70, 70, 70, 45, 36, 17, 8, 17, 1, 8, 1, 1, 1, 1, 1, 1, 109, 150, 161, 161, 161, 161, 161, 109, 70, 45, 45, 36, 36, 17, 17, 17, 1, 150, 150, 150, 150, 150] 201 rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 954 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053946 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053946 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053946/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053946 Building REAL250005053947 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053947' /scratch/stefan/7922901/working/building/REAL250005053947 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053947 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053947/0 /scratch/stefan/7922901/working/building/REAL250005053947 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/57 `/scratch/stefan/7922901/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053947.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053947 none CC(C)=C(F)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 147, 201, 147, 147, 85, 59, 24, 10, 24, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 147, 85, 85, 59, 59, 24, 24, 24, 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: 750 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053947 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053947 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053947/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053947 Building REAL250005053948 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053948' /scratch/stefan/7922901/working/building/REAL250005053948 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053948 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053948/0 /scratch/stefan/7922901/working/building/REAL250005053948 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/58 `/scratch/stefan/7922901/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CCCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053948.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053948 none CN(CCNC(=O)C1=CCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [28, 10, 28, 74, 103, 139, 139, 139, 144, 144, 144, 144, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 74, 74, 103, 103, 139, 144, 144, 144, 144, 144, 144, 144, 1] 144 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: 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: REAL250005053948 none CN(CCNC(=O)C1=CCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [96, 70, 41, 11, 11, 1, 11, 1, 1, 1, 1, 1, 96, 136, 136, 144, 144, 144, 144, 144, 96, 96, 96, 70, 70, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 144] 144 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053948 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053948 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053948/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053948 Building REAL250005053949 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053949' /scratch/stefan/7922901/working/building/REAL250005053949 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053949 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053949/0 /scratch/stefan/7922901/working/building/REAL250005053949 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/59 `/scratch/stefan/7922901/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CN(C)C=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053949.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053949 none CN(CCNC(=O)C1=CN(C)C=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 25, 71, 89, 127, 127, 127, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 71, 71, 89, 89, 127, 201, 201, 201, 201, 201, 201, 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: 635 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: REAL250005053949 none CN(CCNC(=O)C1=CN(C)C=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 28, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 99, 178, 178, 201, 201, 201, 201, 201, 99, 99, 99, 54, 54, 28, 28, 5, 1, 2, 2, 2, 1, 1, 201] 201 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35]) total number of confs: 706 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053949 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053949 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053949/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053949 Building REAL250005053950 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053950' /scratch/stefan/7922901/working/building/REAL250005053950 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053950 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053950/0 /scratch/stefan/7922901/working/building/REAL250005053950 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/60 `/scratch/stefan/7922901/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CN(C)C=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053950.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053950 none CN(CCNC(=O)C1=CN(C)C=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 6, 16, 25, 25, 47, 47, 47, 67, 67, 67, 67, 67, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 25, 25, 25, 25, 47, 67, 67, 67, 67, 67, 1] 67 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: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053950 none CN(CCNC(=O)C1=CN(C)C=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [53, 43, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 53, 67, 67, 67, 67, 67, 67, 67, 53, 53, 53, 43, 43, 27, 27, 7, 1, 2, 2, 2, 1, 67] 67 rigid atoms, others: [33, 5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053950 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053950 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053950/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053950 Building REAL250005053951 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053951' /scratch/stefan/7922901/working/building/REAL250005053951 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053951 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053951/0 /scratch/stefan/7922901/working/building/REAL250005053951 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/61 `/scratch/stefan/7922901/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCCCO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053951.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053951 none CN(CCNC(=O)C1CCCCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 21, 28, 28, 52, 52, 52, 103, 103, 103, 103, 103, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 28, 28, 28, 28, 52, 103, 103, 103, 103, 103, 103, 103, 103, 103, 1] 103 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: 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: REAL250005053951 none CN(CCNC(=O)C1CCCCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [81, 67, 50, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 81, 101, 101, 103, 103, 103, 103, 103, 81, 81, 81, 67, 67, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103] 103 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053951 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053951 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053951/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053951 Building REAL250005053952 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053952' /scratch/stefan/7922901/working/building/REAL250005053952 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053952 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053952/0 /scratch/stefan/7922901/working/building/REAL250005053952 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/62 `/scratch/stefan/7922901/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC1(C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053952.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053952 none CN(CCNC(=O)C1CC1(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 63, 85, 151, 151, 151, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 63, 63, 85, 85, 151, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 739 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: REAL250005053952 none CN(CCNC(=O)C1CC1(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 72, 41, 9, 9, 1, 9, 1, 1, 1, 1, 1, 115, 187, 187, 201, 201, 201, 201, 201, 115, 115, 115, 72, 72, 41, 41, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 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: 741 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053952 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053952 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053952/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053952 Building REAL250005053953 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053953' /scratch/stefan/7922901/working/building/REAL250005053953 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053953 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053953/0 /scratch/stefan/7922901/working/building/REAL250005053953 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/63 `/scratch/stefan/7922901/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053953.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053953 none CCC(C)OCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [193, 191, 190, 191, 180, 146, 146, 146, 89, 61, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 191, 191, 191, 191, 180, 180, 146, 89, 89, 61, 61, 19, 19, 19, 1] 193 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: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053953 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053953 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053953/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053953 Building REAL250005053954 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053954' /scratch/stefan/7922901/working/building/REAL250005053954 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053954 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053954/0 /scratch/stefan/7922901/working/building/REAL250005053954 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/64 `/scratch/stefan/7922901/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1CC1(C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053954.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053954 none CN(CCNC(=O)[C@H]1CC1(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 64, 85, 150, 150, 150, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 64, 64, 85, 85, 150, 201, 201, 201, 201, 201, 201, 201, 201, 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: 735 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: REAL250005053954 none CN(CCNC(=O)[C@H]1CC1(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 71, 41, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 116, 187, 187, 201, 201, 201, 201, 201, 116, 116, 116, 71, 71, 41, 41, 9, 1, 1, 2, 2, 2, 2, 2, 2, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 4, 6, 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: 740 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053954 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053954 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053954/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053954 Building REAL250005053955 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053955' /scratch/stefan/7922901/working/building/REAL250005053955 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053955 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053955/0 /scratch/stefan/7922901/working/building/REAL250005053955 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/65 `/scratch/stefan/7922901/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1CCCO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053955.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053955 none CN(CCNC(=O)[C@@H]1CCCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 21, 28, 28, 49, 49, 49, 79, 79, 79, 79, 79, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 28, 28, 28, 28, 49, 79, 79, 79, 79, 79, 79, 1] 79 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: 251 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: REAL250005053955 none CN(CCNC(=O)[C@@H]1CCCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [69, 58, 45, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 69, 79, 79, 79, 79, 79, 79, 79, 69, 69, 69, 58, 58, 45, 45, 12, 1, 1, 1, 1, 1, 1, 79] 79 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 308 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053955 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053955 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053955/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053955 Building REAL250005053956 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053956' /scratch/stefan/7922901/working/building/REAL250005053956 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053956 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053956/0 /scratch/stefan/7922901/working/building/REAL250005053956 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/66 `/scratch/stefan/7922901/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053956.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053956 none C#CCCCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 170, 168, 154, 48, 48, 48, 44, 31, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 170, 170, 170, 170, 156, 156, 48, 44, 44, 31, 31, 14, 14, 14, 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: 908 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053956 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053956 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053956/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053956 Building REAL250005053957 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053957' /scratch/stefan/7922901/working/building/REAL250005053957 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053957 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053957/0 /scratch/stefan/7922901/working/building/REAL250005053957 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/67 `/scratch/stefan/7922901/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053957.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053957 none CCNC(=O)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 141, 141, 93, 141, 63, 63, 63, 53, 41, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 141, 93, 93, 63, 53, 53, 41, 41, 16, 16, 16, 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: 959 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053957 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053957 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053957/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053957 Building REAL250005053958 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053958' /scratch/stefan/7922901/working/building/REAL250005053958 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053958 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053958/0 /scratch/stefan/7922901/working/building/REAL250005053958 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/68 `/scratch/stefan/7922901/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053958.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053958 none COC(C)CCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 80, 106, 96, 45, 45, 45, 44, 32, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 106, 106, 106, 100, 106, 106, 106, 100, 100, 96, 96, 45, 44, 44, 32, 32, 18, 18, 18, 1] 106 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: 571 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053958 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053958 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053958/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053958 Building REAL250005053959 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053959' /scratch/stefan/7922901/working/building/REAL250005053959 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053959 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053959/0 /scratch/stefan/7922901/working/building/REAL250005053959 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/69 `/scratch/stefan/7922901/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CN=CN=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053959.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053959 none CN(CCNC(=O)C1=CN=CN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [26, 10, 26, 63, 72, 104, 104, 104, 104, 104, 104, 104, 104, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 63, 63, 72, 72, 104, 104, 104, 104, 1] 104 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: 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: REAL250005053959 none CN(CCNC(=O)C1=CN=CN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [60, 37, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 60, 98, 98, 106, 106, 106, 106, 106, 60, 60, 60, 37, 37, 21, 21, 5, 1, 1, 1, 106] 106 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053959 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053959 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053959/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053959 Building REAL250005053960 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053960' /scratch/stefan/7922901/working/building/REAL250005053960 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053960 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053960/0 /scratch/stefan/7922901/working/building/REAL250005053960 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/70 `/scratch/stefan/7922901/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CCOCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053960.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053960 none CN(CCNC(=O)C1=CCOCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 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 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [27, 10, 27, 58, 70, 111, 111, 111, 171, 171, 171, 171, 171, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 58, 58, 70, 70, 111, 171, 171, 171, 171, 171, 171, 171, 1] 171 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: 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: REAL250005053960 none CN(CCNC(=O)C1=CCOCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 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 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [110, 78, 49, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 110, 159, 159, 171, 171, 171, 171, 171, 110, 110, 110, 78, 78, 49, 49, 11, 1, 1, 1, 1, 1, 1, 1, 171] 171 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 654 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053960 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053960 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053960/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053960 Building REAL250005053961 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053961' /scratch/stefan/7922901/working/building/REAL250005053961 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053961 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053961/0 /scratch/stefan/7922901/working/building/REAL250005053961 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/71 `/scratch/stefan/7922901/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1=COC=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053961.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053961 none CN(CCNC(=O)CC1=COC=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 26, 26, 54, 54, 54, 105, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 26, 26, 26, 26, 54, 105, 105, 201, 201, 201, 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: 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: REAL250005053961 none CN(CCNC(=O)CC1=COC=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 12, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 122, 76, 15, 15, 4, 15, 1, 1, 1, 1, 1, 1, 163, 199, 199, 201, 201, 201, 201, 201, 163, 163, 163, 122, 122, 76, 76, 15, 4, 4, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 850 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053961 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053961 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053961/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053961 Building REAL250005053962 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053962' /scratch/stefan/7922901/working/building/REAL250005053962 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053962 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053962/0 /scratch/stefan/7922901/working/building/REAL250005053962 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/72 `/scratch/stefan/7922901/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)=CO1) `REAL250005053962.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053962 none CC1=NC(C(=O)NCCN(C)C(=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.3', '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, 1, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 201, 201, 201, 101, 65, 27, 12, 27, 1, 12, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 101, 101, 65, 65, 27, 27, 27, 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: 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: REAL250005053962 none CC1=NC(C(=O)NCCN(C)C(=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.3', '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, 1, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 4, 4, 4, 25, 47, 93, 93, 161, 161, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 4, 24, 24, 47, 47, 93, 93, 93, 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: 629 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053962 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053962 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053962/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053962 Building REAL250005053963 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053963' /scratch/stefan/7922901/working/building/REAL250005053963 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053963 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053963/0 /scratch/stefan/7922901/working/building/REAL250005053963 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/73 `/scratch/stefan/7922901/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053963.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053963 none C[C@H](NC(N)=O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 55, 75, 75, 75, 75, 75, 55, 55, 34, 27, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 55, 34, 34, 27, 27, 13, 13, 13, 1] 75 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053963 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053963 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053963/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053963 Building REAL250005053964 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053964' /scratch/stefan/7922901/working/building/REAL250005053964 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053964 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053964/0 /scratch/stefan/7922901/working/building/REAL250005053964 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/74 `/scratch/stefan/7922901/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)=CO1) `REAL250005053964.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053964 none CC1=CC(C(=O)NCCN(C)C(=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.3', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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, 141, 141, 141, 99, 71, 26, 10, 26, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 141, 99, 99, 71, 71, 26, 26, 26, 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: 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: REAL250005053964 none CC1=CC(C(=O)NCCN(C)C(=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.3', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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, 5, 5, 5, 31, 59, 105, 105, 179, 179, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 5, 31, 31, 59, 59, 105, 105, 105, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053964 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053964 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053964/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053964 Building REAL250005053965 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053965' /scratch/stefan/7922901/working/building/REAL250005053965 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053965 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053965/0 /scratch/stefan/7922901/working/building/REAL250005053965 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/75 `/scratch/stefan/7922901/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053965.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053965 none CCC(C)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 183, 200, 62, 62, 62, 59, 42, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 200, 200, 186, 186, 62, 59, 59, 42, 42, 17, 17, 17, 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: 865 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053965 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053965 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053965/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053965 Building REAL250005053966 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053966' /scratch/stefan/7922901/working/building/REAL250005053966 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053966 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053966/0 /scratch/stefan/7922901/working/building/REAL250005053966 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/76 `/scratch/stefan/7922901/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053966.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053966 none C#CCCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 144, 145, 51, 51, 51, 42, 38, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 201, 187, 189, 174, 174, 147, 147, 51, 42, 42, 38, 38, 18, 18, 18, 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: 1029 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053966 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053966 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053966/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053966 Building REAL250005053967 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053967' /scratch/stefan/7922901/working/building/REAL250005053967 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053967 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053967/0 /scratch/stefan/7922901/working/building/REAL250005053967 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/77 `/scratch/stefan/7922901/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC(C)(C)O)C(=O)C1=CC(=O)[N-]O1) `REAL250005053967.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053967 none CN(CCNC(=O)CC(C)(C)O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 525 conformations in input total number of sets (complete confs): 525 using faster count positions algorithm for large data unique positions, atoms: [25, 10, 25, 50, 63, 105, 105, 105, 159, 173, 175, 175, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 50, 50, 63, 63, 105, 159, 159, 175, 175, 175, 175, 175, 175, 525, 1] 525 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: 1278 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053967 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053967 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053967/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053967 Building REAL250005053968 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053968' /scratch/stefan/7922901/working/building/REAL250005053968 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053968 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053968/0 /scratch/stefan/7922901/working/building/REAL250005053968 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/78 `/scratch/stefan/7922901/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005053968.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053968 none COC(C(=O)NCCN(C)C(=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.3', '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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 20, 20, 20, 62, 81, 105, 105, 170, 170, 201, 201, 201, 201, 201, 1, 1, 1, 10, 10, 10, 5, 20, 62, 62, 81, 81, 105, 105, 105, 201, 1, 1, 1, 1, 1] 201 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: 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: REAL250005053968 none COC(C(=O)NCCN(C)C(=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.3', '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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 143, 76, 76, 76, 63, 40, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 143, 201, 201, 154, 154, 154, 143, 76, 63, 63, 40, 40, 19, 19, 19, 1, 201, 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, 38]) total number of confs: 909 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053968 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053968 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053968/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053968 Building REAL250005053969 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053969' /scratch/stefan/7922901/working/building/REAL250005053969 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053969 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053969/0 /scratch/stefan/7922901/working/building/REAL250005053969 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/79 `/scratch/stefan/7922901/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CN=NN1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053969.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053969 none CN(CCNC(=O)C1=CN=NN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 10, 26, 49, 65, 123, 123, 123, 155, 155, 155, 155, 155, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 49, 49, 65, 65, 123, 155, 155, 155, 155, 1] 155 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: 477 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: REAL250005053969 none CN(CCNC(=O)C1=CN=NN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [102, 70, 44, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 102, 145, 145, 155, 155, 155, 155, 155, 102, 102, 102, 70, 70, 44, 44, 10, 1, 2, 2, 2, 155] 155 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 563 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053969 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053969 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053969/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053969 Building REAL250005053970 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053970' /scratch/stefan/7922901/working/building/REAL250005053970 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053970 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053970/0 /scratch/stefan/7922901/working/building/REAL250005053970 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/80 `/scratch/stefan/7922901/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053970.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053970 none CCCCC(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 141, 61, 141, 61, 61, 43, 36, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 175, 175, 175, 175, 141, 141, 141, 141, 61, 43, 43, 36, 36, 16, 16, 16, 1] 175 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: 790 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053970 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053970 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053970/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053970 Building REAL250005053971 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053971' /scratch/stefan/7922901/working/building/REAL250005053971 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053971 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053971/0 /scratch/stefan/7922901/working/building/REAL250005053971 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/81 `/scratch/stefan/7922901/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC(C)(C)C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053971.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053971 none CN(CCNC(=O)C1CC(C)(C)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 29, 73, 98, 170, 170, 170, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 73, 73, 98, 98, 170, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005053971 none CN(CCNC(=O)C1CC(C)(C)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 45, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 81, 182, 182, 201, 201, 201, 201, 201, 81, 81, 81, 45, 45, 23, 23, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 201] 201 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 12, 39, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 653 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053971 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053971 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053971/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053971 Building REAL250005053972 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053972' /scratch/stefan/7922901/working/building/REAL250005053972 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053972 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053972/0 /scratch/stefan/7922901/working/building/REAL250005053972 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/82 `/scratch/stefan/7922901/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053972.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053972 none CC(C)[C@@H](O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 170, 201, 118, 170, 170, 118, 118, 58, 45, 22, 10, 22, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 510, 118, 58, 58, 45, 45, 22, 22, 22, 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: 1322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053972 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053972 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053972/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053972 Building REAL250005053973 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053973' /scratch/stefan/7922901/working/building/REAL250005053973 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053973 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053973/0 /scratch/stefan/7922901/working/building/REAL250005053973 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/83 `/scratch/stefan/7922901/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CN(C)N=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053973.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053973 none CN(CCNC(=O)C1=CN(C)N=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 23, 23, 38, 38, 38, 46, 46, 46, 46, 46, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 23, 23, 23, 23, 38, 46, 46, 46, 46, 1] 46 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: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053973 none CN(CCNC(=O)C1=CN(C)N=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [38, 32, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 38, 46, 46, 46, 46, 46, 46, 46, 38, 38, 38, 32, 32, 22, 22, 6, 1, 2, 2, 2, 46] 46 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053973 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053973 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053973/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053973 Building REAL250005053974 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053974' /scratch/stefan/7922901/working/building/REAL250005053974 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053974 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053974/0 /scratch/stefan/7922901/working/building/REAL250005053974 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/84 `/scratch/stefan/7922901/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NN(C)C=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053974.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053974 none CN(CCNC(=O)C1=NN(C)C=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 6, 16, 17, 17, 29, 29, 29, 45, 45, 45, 45, 45, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 17, 17, 17, 17, 29, 45, 45, 45, 45, 1] 45 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: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053974 none CN(CCNC(=O)C1=NN(C)C=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 37, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 41, 45, 45, 45, 45, 45, 45, 45, 41, 41, 41, 37, 37, 29, 29, 7, 2, 2, 2, 1, 45] 45 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053974 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053974 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053974/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053974 Building REAL250005053975 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053975' /scratch/stefan/7922901/working/building/REAL250005053975 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053975 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053975/0 /scratch/stefan/7922901/working/building/REAL250005053975 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/85 `/scratch/stefan/7922901/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC1(F)F)C(=O)C1=CC(=O)[N-]O1) `REAL250005053975.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053975 none CN(CCNC(=O)C1CC1(F)F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 8, 23, 46, 55, 95, 95, 95, 173, 173, 173, 173, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 46, 46, 55, 55, 95, 173, 173, 173, 1] 173 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: 585 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053975 none CN(CCNC(=O)C1CC1(F)F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [133, 91, 59, 13, 13, 1, 13, 1, 1, 1, 1, 1, 133, 172, 172, 173, 173, 173, 173, 173, 133, 133, 133, 91, 91, 59, 59, 13, 1, 1, 1, 173] 173 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 682 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053975 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053975 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053975/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053975 Building REAL250005053976 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053976' /scratch/stefan/7922901/working/building/REAL250005053976 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053976 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053976/0 /scratch/stefan/7922901/working/building/REAL250005053976 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/86 `/scratch/stefan/7922901/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053976.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053976 none CCC(C)=CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 112, 112, 112, 79, 79, 79, 44, 36, 16, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 112, 112, 112, 112, 79, 44, 44, 36, 36, 16, 16, 16, 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: 962 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053976 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053976 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053976/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053976 Building REAL250005053977 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053977' /scratch/stefan/7922901/working/building/REAL250005053977 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053977 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053977/0 /scratch/stefan/7922901/working/building/REAL250005053977 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/87 `/scratch/stefan/7922901/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053977.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053977 none CC(C)C#CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 132, 94, 70, 33, 10, 33, 1, 10, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 132, 132, 132, 94, 94, 70, 70, 33, 33, 33, 1] 132 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: 519 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053977 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053977 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053977/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053977 Building REAL250005053978 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053978' /scratch/stefan/7922901/working/building/REAL250005053978 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053978 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053978/0 /scratch/stefan/7922901/working/building/REAL250005053978 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/88 `/scratch/stefan/7922901/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1(O)CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053978.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053978 none CN(CCNC(=O)CC1(O)CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 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: [28, 9, 28, 60, 74, 117, 117, 117, 188, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 60, 60, 74, 74, 117, 188, 188, 603, 201, 201, 201, 201, 201, 201, 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: 1406 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: REAL250005053978 none CN(CCNC(=O)CC1(O)CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 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: [145, 113, 80, 25, 25, 8, 25, 1, 1, 1, 1, 1, 1, 145, 193, 193, 201, 201, 201, 201, 201, 145, 145, 145, 113, 113, 80, 80, 25, 8, 8, 6, 1, 1, 1, 1, 1, 1, 201] 603 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 788 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053978 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053978 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053978/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053978 Building REAL250005053979 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053979' /scratch/stefan/7922901/working/building/REAL250005053979 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053979 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053979/0 /scratch/stefan/7922901/working/building/REAL250005053979 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/89 `/scratch/stefan/7922901/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNN=C1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053979.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053979 none CC1=CNN=C1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 195, 195, 195, 88, 58, 27, 10, 27, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 195, 88, 88, 58, 58, 27, 27, 27, 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: 700 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: REAL250005053979 none CC1=CNN=C1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 23, 46, 93, 93, 167, 167, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 3, 23, 23, 46, 46, 94, 94, 94, 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: 669 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053979 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053979 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053979/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053979 Building REAL250005053980 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053980' /scratch/stefan/7922901/working/building/REAL250005053980 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053980 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053980/0 /scratch/stefan/7922901/working/building/REAL250005053980 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/90 `/scratch/stefan/7922901/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)=C1CCC1) `REAL250005053980.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053980 none CC(C(=O)NCCN(C)C(=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.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 47, 81, 118, 118, 190, 190, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 9, 47, 47, 81, 81, 118, 118, 118, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 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: 753 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: REAL250005053980 none CC(C(=O)NCCN(C)C(=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.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 114, 114, 114, 70, 55, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 114, 70, 70, 55, 55, 17, 17, 17, 1, 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]) total number of confs: 704 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053980 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053980 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053980/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053980 Building REAL250005053981 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053981' /scratch/stefan/7922901/working/building/REAL250005053981 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053981 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053981/0 /scratch/stefan/7922901/working/building/REAL250005053981 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/91 `/scratch/stefan/7922901/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C#CC1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053981.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053981 none CN(CCNC(=O)C#CC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 10, 29, 62, 84, 122, 122, 122, 122, 122, 122, 122, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 62, 62, 84, 84, 122, 122, 122, 122, 122, 122, 1] 122 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: 485 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: REAL250005053981 none CN(CCNC(=O)C#CC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [46, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 105, 105, 122, 122, 122, 122, 122, 47, 47, 47, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 122] 122 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29, 30, 31] set([0, 1, 2, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 387 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053981 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053981 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053981/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053981 Building REAL250005053982 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053982' /scratch/stefan/7922901/working/building/REAL250005053982 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053982 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053982/0 /scratch/stefan/7922901/working/building/REAL250005053982 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/92 `/scratch/stefan/7922901/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C#CC(C)(C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053982.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053982 none CN(CCNC(=O)C#CC(C)(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 10, 31, 67, 91, 133, 133, 133, 133, 133, 133, 133, 133, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 31, 67, 67, 91, 91, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 1] 133 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: 523 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053982 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053982 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053982/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053982 Building REAL250005053983 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053983' /scratch/stefan/7922901/working/building/REAL250005053983 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053983 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053983/0 /scratch/stefan/7922901/working/building/REAL250005053983 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/93 `/scratch/stefan/7922901/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1C[C@H]1[N+](=O)[O-])C(=O)C1=CC(=O)[N-]O1) `REAL250005053983.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053983 none CN(CCNC(=O)[C@@H]1C[C@H]1[N+](=O)[O-])C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 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: [20, 7, 20, 38, 42, 91, 91, 91, 201, 201, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 38, 38, 42, 42, 91, 201, 201, 1] 201 rigid atoms, others: [33, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 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: REAL250005053983 none CN(CCNC(=O)[C@@H]1C[C@H]1[N+](=O)[O-])C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 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: [146, 99, 61, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 7, 7, 146, 192, 192, 201, 201, 201, 201, 201, 146, 146, 146, 99, 99, 61, 61, 13, 1, 1, 201] 201 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 793 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053983 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053983 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053983/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053983 Building REAL250005053984 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053984' /scratch/stefan/7922901/working/building/REAL250005053984 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053984 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053984/0 /scratch/stefan/7922901/working/building/REAL250005053984 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/94 `/scratch/stefan/7922901/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCNC(N)=O)C(=O)C1=CC(=O)[N-]O1) `REAL250005053984.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053984 none CN(CCNC(=O)CCNC(N)=O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 4, 6, 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, 9, 19, 29, 29, 51, 51, 51, 106, 162, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 29, 29, 29, 29, 51, 106, 106, 162, 162, 201, 201, 201, 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/7922901/working/building/REAL250005053984 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053984 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053984/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053984 Building REAL250005053985 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053985' /scratch/stefan/7922901/working/building/REAL250005053985 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053985 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053985/0 /scratch/stefan/7922901/working/building/REAL250005053985 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/95 `/scratch/stefan/7922901/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005053985.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053985 none CC1CCC(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 110, 110, 110, 69, 57, 22, 10, 22, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 69, 69, 57, 57, 22, 22, 22, 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: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053985 none CC1CCC(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 42, 66, 104, 104, 183, 183, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 42, 42, 66, 66, 104, 104, 104, 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: 714 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053985 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053985 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053985/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053985 Building REAL250005053986 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053986' /scratch/stefan/7922901/working/building/REAL250005053986 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053986 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053986/0 /scratch/stefan/7922901/working/building/REAL250005053986 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/96 `/scratch/stefan/7922901/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053986.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053986 none C#CCOCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 124, 124, 124, 57, 57, 57, 33, 27, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 124, 124, 124, 124, 57, 33, 33, 27, 27, 13, 13, 13, 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: 888 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053986 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053986 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053986/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053986 Building REAL250005053987 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053987' /scratch/stefan/7922901/working/building/REAL250005053987 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053987 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053987/0 /scratch/stefan/7922901/working/building/REAL250005053987 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/97 `/scratch/stefan/7922901/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053987.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053987 none C#CCOC(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 161, 95, 161, 95, 95, 58, 42, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 161, 161, 161, 161, 95, 58, 58, 42, 42, 17, 17, 17, 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: 903 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053987 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053987 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053987/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053987 Building REAL250005053988 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053988' /scratch/stefan/7922901/working/building/REAL250005053988 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053988 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053988/0 /scratch/stefan/7922901/working/building/REAL250005053988 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/98 `/scratch/stefan/7922901/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053988.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053988 none C=CCC(C)(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 101, 45, 101, 101, 45, 45, 37, 33, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 101, 101, 101, 101, 101, 101, 45, 37, 37, 33, 33, 15, 15, 15, 1] 143 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: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053988 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053988 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053988/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053988 Building REAL250005053989 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053989' /scratch/stefan/7922901/working/building/REAL250005053989 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053989 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053989/0 /scratch/stefan/7922901/working/building/REAL250005053989 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/99 `/scratch/stefan/7922901/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC12CCC2)C(=O)C1=CC(=O)[N-]O1) `REAL250005053989.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053989 none CN(CCNC(=O)C1CC12CCC2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 53, 64, 100, 100, 100, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 25, 53, 53, 64, 64, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 676 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053989 none CN(CCNC(=O)C1CC12CCC2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 94, 57, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 136, 191, 191, 201, 201, 201, 201, 201, 136, 136, 136, 94, 94, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38]) total number of confs: 782 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053989 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053989 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053989/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053989 Building REAL250005053990 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053990' /scratch/stefan/7922901/working/building/REAL250005053990 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053990 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053990/0 /scratch/stefan/7922901/working/building/REAL250005053990 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/100 `/scratch/stefan/7922901/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053990.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053990 none CN(C)C(=O)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 75, 111, 61, 61, 61, 49, 33, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 75, 75, 61, 49, 49, 33, 33, 14, 14, 14, 1] 111 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: 473 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053990 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053990 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053990/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053990 Building REAL250005053991 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053991' /scratch/stefan/7922901/working/building/REAL250005053991 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053991 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053991/0 /scratch/stefan/7922901/working/building/REAL250005053991 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/101 `/scratch/stefan/7922901/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NN(C)C=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053991.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053991 none CN(CCNC(=O)C1=NN(C)C=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 6, 18, 27, 27, 45, 45, 45, 67, 67, 67, 67, 67, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 27, 27, 27, 27, 45, 67, 67, 67, 67, 67, 1] 67 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: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053991 none CN(CCNC(=O)C1=NN(C)C=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [49, 43, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 49, 67, 67, 67, 67, 67, 67, 67, 49, 49, 49, 43, 43, 31, 31, 11, 2, 2, 2, 1, 1, 67] 67 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053991 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053991 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053991/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053991 Building REAL250005053992 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053992' /scratch/stefan/7922901/working/building/REAL250005053992 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053992 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053992/0 /scratch/stefan/7922901/working/building/REAL250005053992 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/102 `/scratch/stefan/7922901/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053992.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053992 none COCCC(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 103, 100, 68, 100, 68, 68, 55, 41, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 103, 103, 100, 100, 100, 100, 68, 55, 55, 41, 41, 16, 16, 16, 1] 108 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: 495 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053992 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053992 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053992/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053992 Building REAL250005053993 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053993' /scratch/stefan/7922901/working/building/REAL250005053993 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053993 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053993/0 /scratch/stefan/7922901/working/building/REAL250005053993 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/103 `/scratch/stefan/7922901/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CN1N=CN=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053993.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053993 none CN(CCNC(=O)CN1N=CN=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.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', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 18, 25, 25, 55, 55, 55, 139, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 25, 25, 25, 25, 55, 139, 139, 201, 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: 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: REAL250005053993 none CN(CCNC(=O)CN1N=CN=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.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', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 8, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 171, 141, 51, 51, 9, 51, 1, 1, 1, 1, 1, 1, 189, 201, 201, 201, 201, 201, 201, 201, 189, 189, 189, 171, 171, 141, 141, 51, 9, 9, 1, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32]) total number of confs: 798 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053993 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053993 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053993/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053993 Building REAL250005053994 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053994' /scratch/stefan/7922901/working/building/REAL250005053994 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053994 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053994/0 /scratch/stefan/7922901/working/building/REAL250005053994 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/104 `/scratch/stefan/7922901/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053994.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053994 none CCCC[C@@H](C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 181, 145, 63, 145, 145, 63, 63, 42, 35, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 181, 181, 181, 181, 145, 145, 145, 63, 42, 42, 35, 35, 16, 16, 16, 1] 181 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: 816 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053994 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053994 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053994/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053994 Building REAL250005053995 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053995' /scratch/stefan/7922901/working/building/REAL250005053995 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053995 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053995/0 /scratch/stefan/7922901/working/building/REAL250005053995 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/105 `/scratch/stefan/7922901/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053995.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053995 none CCC(C)(C)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 102, 193, 193, 61, 61, 61, 51, 39, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 197, 197, 197, 197, 108, 108, 61, 51, 51, 39, 39, 16, 16, 16, 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: 985 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053995 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053995 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053995/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053995 Building REAL250005053996 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053996' /scratch/stefan/7922901/working/building/REAL250005053996 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053996 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053996/0 /scratch/stefan/7922901/working/building/REAL250005053996 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/106 `/scratch/stefan/7922901/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053996.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053996 none CC(C)C(C)(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 106, 183, 183, 106, 106, 64, 50, 21, 10, 21, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 183, 183, 183, 106, 64, 64, 50, 50, 21, 21, 21, 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: 904 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053996 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053996 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053996/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053996 Building REAL250005053997 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053997' /scratch/stefan/7922901/working/building/REAL250005053997 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053997 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053997/0 /scratch/stefan/7922901/working/building/REAL250005053997 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/107 `/scratch/stefan/7922901/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005053997.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053997 none C=CC(C)(C)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 134, 169, 169, 100, 100, 100, 68, 44, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 169, 169, 169, 169, 169, 136, 136, 100, 68, 68, 44, 44, 16, 16, 16, 1] 169 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: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053997 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053997 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053997/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053997 Building REAL250005053998 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053998' /scratch/stefan/7922901/working/building/REAL250005053998 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053998 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053998/0 /scratch/stefan/7922901/working/building/REAL250005053998 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/108 `/scratch/stefan/7922901/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CN1N=CC=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053998.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053998 none CN(CCNC(=O)CN1N=CC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 31, 31, 75, 75, 75, 191, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 31, 31, 31, 31, 75, 191, 191, 201, 201, 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: 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: REAL250005053998 none CN(CCNC(=O)CN1N=CC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 149, 105, 31, 31, 5, 31, 1, 1, 1, 1, 1, 1, 171, 201, 201, 201, 201, 201, 201, 201, 171, 171, 171, 149, 149, 105, 105, 31, 5, 5, 1, 1, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/7922901/working/building/REAL250005053998 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053998 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053998/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053998 Building REAL250005053999 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005053999' /scratch/stefan/7922901/working/building/REAL250005053999 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005053999 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005053999/0 /scratch/stefan/7922901/working/building/REAL250005053999 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/109 `/scratch/stefan/7922901/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1C[C@H]1C1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005053999.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005053999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005053999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053999 none CN(CCNC(=O)[C@@H]1C[C@H]1C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 27, 31, 57, 57, 57, 167, 167, 167, 167, 167, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 27, 27, 31, 31, 57, 167, 167, 201, 201, 201, 201, 201, 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: 625 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053999 none CN(CCNC(=O)[C@@H]1C[C@H]1C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 159, 118, 42, 42, 6, 42, 6, 6, 6, 1, 6, 1, 1, 1, 181, 200, 200, 201, 201, 201, 201, 201, 181, 181, 181, 159, 159, 118, 118, 42, 6, 6, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 812 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005053999 none CN(CCNC(=O)[C@@H]1C[C@H]1C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 102, 62, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 140, 165, 165, 167, 167, 167, 167, 167, 140, 140, 140, 102, 102, 62, 62, 12, 1, 1, 6, 6, 6, 6, 6, 167] 201 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 693 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005053999 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005053999 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005053999/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005053999 Building REAL250005054000 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054000' /scratch/stefan/7922901/working/building/REAL250005054000 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054000 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054000/0 /scratch/stefan/7922901/working/building/REAL250005054000 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/110 `/scratch/stefan/7922901/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CC)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054000.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054000 none CCC(C)(CC)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 181, 123, 181, 181, 187, 123, 123, 85, 69, 22, 10, 22, 1, 10, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 181, 181, 181, 197, 197, 197, 197, 197, 123, 85, 85, 69, 69, 22, 22, 22, 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: 1071 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054000 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054000 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054000/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054000 Building REAL250005054001 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054001' /scratch/stefan/7922901/working/building/REAL250005054001 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054001 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054001/0 /scratch/stefan/7922901/working/building/REAL250005054001 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/111 `/scratch/stefan/7922901/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054001.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054001 none C=C(C)CCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 151, 57, 57, 57, 43, 37, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 156, 153, 153, 154, 156, 157, 157, 155, 155, 57, 43, 43, 37, 37, 16, 16, 16, 1] 157 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: 709 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054001 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054001 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054001/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054001 Building REAL250005054002 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054002' /scratch/stefan/7922901/working/building/REAL250005054002 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054002 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054002/0 /scratch/stefan/7922901/working/building/REAL250005054002 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/112 `/scratch/stefan/7922901/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC=NS1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054002.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054002 none CN(CCNC(=O)C1=CC=NS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 9, 20, 39, 43, 54, 54, 54, 83, 83, 83, 83, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 39, 39, 43, 43, 54, 83, 83, 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: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054002 none CN(CCNC(=O)C1=CC=NS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [50, 33, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 50, 83, 83, 83, 83, 83, 83, 83, 50, 50, 50, 33, 33, 20, 20, 6, 1, 1, 83] 83 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054002 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054002 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054002/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054002 Building REAL250005054003 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054003' /scratch/stefan/7922901/working/building/REAL250005054003 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054003 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054003/0 /scratch/stefan/7922901/working/building/REAL250005054003 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/113 `/scratch/stefan/7922901/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]12C[C@H]1COC2)C(=O)C1=CC(=O)[N-]O1) `REAL250005054003.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054003 none CN(CCNC(=O)[C@]12C[C@H]1COC2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 51, 63, 89, 89, 89, 201, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 51, 51, 63, 63, 89, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 499 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: REAL250005054003 none CN(CCNC(=O)[C@]12C[C@H]1COC2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 61, 33, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 107, 189, 189, 201, 201, 201, 201, 201, 107, 107, 107, 61, 61, 33, 33, 6, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 734 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054003 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054003 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054003/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054003 Building REAL250005054004 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054004' /scratch/stefan/7922901/working/building/REAL250005054004 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054004 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054004/0 /scratch/stefan/7922901/working/building/REAL250005054004 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/114 `/scratch/stefan/7922901/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(C)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054004.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054004 none CN(CCNC(=O)C1(C)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [21, 8, 21, 48, 60, 90, 90, 90, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 48, 48, 60, 60, 90, 201, 201, 201, 201, 201, 201, 201, 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: 655 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: REAL250005054004 none CN(CCNC(=O)C1(C)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [108, 67, 36, 7, 7, 1, 7, 1, 1, 1, 1, 108, 191, 191, 201, 201, 201, 201, 201, 108, 108, 108, 67, 67, 36, 36, 7, 2, 2, 2, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 744 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054004 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054004 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054004/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054004 Building REAL250005054005 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054005' /scratch/stefan/7922901/working/building/REAL250005054005 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054005 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054005/0 /scratch/stefan/7922901/working/building/REAL250005054005 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/115 `/scratch/stefan/7922901/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054005.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054005 none CNC(=O)NCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [159, 151, 151, 151, 135, 71, 71, 71, 58, 38, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 151, 135, 135, 71, 58, 58, 38, 38, 16, 16, 16, 1] 159 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: 696 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054005 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054005 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054005/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054005 Building REAL250005054006 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054006' /scratch/stefan/7922901/working/building/REAL250005054006 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054006 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054006/0 /scratch/stefan/7922901/working/building/REAL250005054006 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/116 `/scratch/stefan/7922901/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1CCCO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054006.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054006 none CN(CCNC(=O)[C@H]1CCCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 27, 27, 41, 41, 41, 75, 75, 75, 75, 75, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 41, 75, 75, 75, 75, 75, 75, 1] 75 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: 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: REAL250005054006 none CN(CCNC(=O)[C@H]1CCCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [63, 59, 45, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 63, 75, 75, 75, 75, 75, 75, 75, 63, 63, 63, 59, 59, 45, 45, 11, 1, 1, 1, 1, 1, 1, 75] 75 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054006 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054006 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054006/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054006 Building REAL250005054007 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054007' /scratch/stefan/7922901/working/building/REAL250005054007 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054007 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054007/0 /scratch/stefan/7922901/working/building/REAL250005054007 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/117 `/scratch/stefan/7922901/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005054007.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054007 none CC(CC(=O)NCCN(C)C(=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.3', '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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 2, 7, 20, 20, 20, 45, 58, 81, 81, 116, 116, 127, 127, 127, 127, 127, 1, 1, 1, 3, 3, 3, 2, 7, 7, 20, 45, 45, 58, 58, 81, 81, 81, 127, 1, 1, 1, 1, 1] 127 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: 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: REAL250005054007 none CC(CC(=O)NCCN(C)C(=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.3', '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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 125, 51, 51, 51, 44, 36, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 125, 126, 126, 51, 44, 44, 36, 36, 16, 16, 16, 1, 127, 127, 127, 127, 127] 127 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: 537 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054007 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054007 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054007/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054007 Building REAL250005054008 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054008' /scratch/stefan/7922901/working/building/REAL250005054008 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054008 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054008/0 /scratch/stefan/7922901/working/building/REAL250005054008 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/118 `/scratch/stefan/7922901/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(C)(C)C(N)=O)C(=O)C1=CC(=O)[N-]O1) `REAL250005054008.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054008 none CN(CCNC(=O)C(C)(C)C(N)=O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 30, 32, 65, 65, 65, 142, 142, 142, 167, 167, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 30, 30, 32, 32, 65, 142, 142, 142, 142, 142, 142, 167, 167, 1] 167 rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 656 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054008 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054008 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054008/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054008 Building REAL250005054009 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054009' /scratch/stefan/7922901/working/building/REAL250005054009 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054009 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054009/0 /scratch/stefan/7922901/working/building/REAL250005054009 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/119 `/scratch/stefan/7922901/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(C2CC2)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054009.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054009 none CN(CCNC(=O)C1(C2CC2)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 32, 35, 58, 58, 58, 120, 201, 201, 120, 120, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 32, 32, 35, 35, 58, 201, 201, 201, 201, 201, 120, 120, 120, 120, 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: 690 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054009 none CN(CCNC(=O)C1(C2CC2)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 125, 88, 24, 24, 10, 24, 1, 1, 1, 1, 10, 10, 154, 197, 197, 201, 201, 201, 201, 201, 154, 154, 154, 125, 125, 88, 88, 24, 1, 1, 1, 1, 1, 10, 10, 10, 10, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38]) total number of confs: 821 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: REAL250005054009 none CN(CCNC(=O)C1(C2CC2)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 48, 26, 5, 5, 1, 5, 1, 1, 10, 10, 1, 1, 78, 110, 110, 120, 120, 120, 120, 120, 78, 78, 78, 48, 48, 26, 26, 5, 10, 10, 10, 10, 10, 1, 1, 1, 1, 120] 201 rigid atoms, others: [34, 35, 36, 5, 7, 8, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 467 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054009 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054009 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054009/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054009 Building REAL250005054010 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054010' /scratch/stefan/7922901/working/building/REAL250005054010 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054010 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054010/0 /scratch/stefan/7922901/working/building/REAL250005054010 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/120 `/scratch/stefan/7922901/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054010.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054010 none COC1CC(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 116, 116, 116, 69, 56, 20, 10, 20, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 116, 69, 69, 56, 56, 20, 20, 20, 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: 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: REAL250005054010 none COC1CC(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 9, 39, 66, 96, 96, 182, 182, 201, 201, 201, 201, 201, 1, 4, 4, 4, 1, 1, 1, 1, 9, 39, 39, 66, 66, 96, 96, 96, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 20, 24, 25, 26, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054010 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054010 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054010/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054010 Building REAL250005054011 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054011' /scratch/stefan/7922901/working/building/REAL250005054011 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054011 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054011/0 /scratch/stefan/7922901/working/building/REAL250005054011 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/121 `/scratch/stefan/7922901/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054011.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054011 none C=CCCOCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 131, 125, 108, 51, 51, 51, 29, 25, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 131, 131, 108, 108, 51, 29, 29, 25, 25, 13, 13, 13, 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: 908 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054011 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054011 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054011/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054011 Building REAL250005054012 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054012' /scratch/stefan/7922901/working/building/REAL250005054012 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054012 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054012/0 /scratch/stefan/7922901/working/building/REAL250005054012 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/122 `/scratch/stefan/7922901/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054012.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054012 none C=CCOC(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 95, 60, 95, 60, 60, 54, 41, 18, 8, 18, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 95, 95, 95, 95, 60, 54, 54, 41, 41, 18, 18, 18, 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: 894 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054012 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054012 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054012/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054012 Building REAL250005054013 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054013' /scratch/stefan/7922901/working/building/REAL250005054013 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054013 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054013/0 /scratch/stefan/7922901/working/building/REAL250005054013 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/123 `/scratch/stefan/7922901/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NSC=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054013.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054013 none CN(CCNC(=O)C1=NSC=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', '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: [5, 8, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 18, 25, 25, 41, 41, 41, 57, 57, 57, 57, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 25, 25, 25, 25, 41, 57, 57, 1] 57 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: 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: REAL250005054013 none CN(CCNC(=O)C1=NSC=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', '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: [5, 8, 5, 5, 8, 1, 11, 1, 8, 14, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [45, 41, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 45, 57, 57, 57, 57, 57, 57, 57, 45, 45, 45, 41, 41, 30, 30, 9, 1, 1, 57] 57 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054013 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054013 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054013/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054013 Building REAL250005054014 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054014' /scratch/stefan/7922901/working/building/REAL250005054014 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054014 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054014/0 /scratch/stefan/7922901/working/building/REAL250005054014 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/124 `/scratch/stefan/7922901/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C1CCC1) `REAL250005054014.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054014 none CC(C(=O)NCCN(C)C(=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.3', '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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 12, 12, 12, 45, 62, 83, 83, 118, 118, 128, 128, 128, 128, 128, 1, 1, 1, 1, 3, 3, 3, 3, 12, 45, 45, 62, 62, 83, 83, 83, 128, 1, 1, 1, 1, 1, 1, 1] 128 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: 468 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054014 none CC(C(=O)NCCN(C)C(=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.3', '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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 77, 77, 77, 61, 44, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 128, 128, 128, 128, 77, 61, 61, 44, 44, 17, 17, 17, 1, 128, 128, 128, 128, 128, 128, 128] 128 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: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054014 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054014 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054014/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054014 Building REAL250005054015 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054015' /scratch/stefan/7922901/working/building/REAL250005054015 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054015 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054015/0 /scratch/stefan/7922901/working/building/REAL250005054015 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/125 `/scratch/stefan/7922901/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CO1) `REAL250005054015.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054015 none CC1CC(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 128, 128, 79, 62, 22, 10, 22, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 79, 79, 62, 62, 22, 22, 22, 1, 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]) total number of confs: 702 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: REAL250005054015 none CC1CC(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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 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, 8, 8, 40, 70, 112, 112, 185, 185, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 40, 40, 70, 70, 112, 112, 112, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 19, 20, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 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/7922901/working/building/REAL250005054015 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054015 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054015/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054015 Building REAL250005054016 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054016' /scratch/stefan/7922901/working/building/REAL250005054016 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054016 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054016/0 /scratch/stefan/7922901/working/building/REAL250005054016 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/126 `/scratch/stefan/7922901/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCCC(N)=O)C(=O)C1=CC(=O)[N-]O1) `REAL250005054016.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054016 none CN(CCNC(=O)CCCC(N)=O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 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: [15, 8, 15, 29, 29, 35, 35, 35, 96, 113, 194, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 29, 29, 29, 29, 35, 96, 96, 136, 136, 182, 182, 201, 201, 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: 1008 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054016 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054016 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054016/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054016 Building REAL250005054017 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054017' /scratch/stefan/7922901/working/building/REAL250005054017 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054017 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054017/0 /scratch/stefan/7922901/working/building/REAL250005054017 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/127 `/scratch/stefan/7922901/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(F)CCCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054017.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054017 none CN(CCNC(=O)C1(F)CCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 8, 17, 23, 23, 44, 44, 44, 80, 80, 80, 80, 80, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 23, 23, 23, 23, 44, 80, 80, 80, 80, 80, 80, 80, 80, 1] 80 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: 255 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: REAL250005054017 none CN(CCNC(=O)C1(F)CCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [61, 49, 41, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 61, 80, 80, 80, 80, 80, 80, 80, 61, 61, 61, 49, 49, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 80] 80 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 302 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054017 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054017 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054017/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054017 Building REAL250005054018 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054018' /scratch/stefan/7922901/working/building/REAL250005054018 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054018 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054018/0 /scratch/stefan/7922901/working/building/REAL250005054018 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/128 `/scratch/stefan/7922901/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CN=CN1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054018.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054018 none CN(CCNC(=O)C1=CN=CN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 26, 55, 82, 148, 148, 148, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 26, 55, 55, 82, 82, 148, 201, 201, 201, 201, 201, 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: 610 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054018 none CN(CCNC(=O)C1=CN=CN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 89, 51, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 129, 191, 191, 201, 201, 201, 201, 201, 129, 129, 129, 89, 89, 51, 51, 11, 1, 1, 2, 2, 2, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 761 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054018 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054018 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054018/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054018 Building REAL250005054019 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054019' /scratch/stefan/7922901/working/building/REAL250005054019 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054019 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054019/0 /scratch/stefan/7922901/working/building/REAL250005054019 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/129 `/scratch/stefan/7922901/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C(C)(C)C) `REAL250005054019.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054019 none CC(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 158, 158, 158, 106, 87, 35, 12, 35, 1, 12, 1, 1, 1, 1, 1, 1, 179, 183, 183, 179, 183, 183, 183, 183, 158, 106, 106, 87, 87, 35, 35, 35, 1, 183, 183, 183, 183, 183, 183, 183, 183, 183] 183 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: 793 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054019 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054019 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054019/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054019 Building REAL250005054020 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054020' /scratch/stefan/7922901/working/building/REAL250005054020 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054020 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054020/0 /scratch/stefan/7922901/working/building/REAL250005054020 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/130 `/scratch/stefan/7922901/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NNN=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054020.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054020 none CN(CCNC(=O)C1=NNN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.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: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 18, 27, 27, 35, 35, 35, 55, 55, 55, 55, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 27, 27, 27, 27, 35, 55, 55, 1] 55 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: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054020 none CN(CCNC(=O)C1=NNN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.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: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [37, 33, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 37, 55, 55, 55, 55, 55, 55, 55, 37, 37, 37, 33, 33, 25, 25, 7, 1, 1, 55] 55 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054020 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054020/1 /scratch/stefan/7922901/working/building/REAL250005054020 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/131 `/scratch/stefan/7922901/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CN=NN1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054020.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054020 none CN(CCNC(=O)C1=CN=NN1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 13, 13, 15, 15, 15, 19, 19, 19, 19, 1, 8, 1, 1, 1, 1, 1, 1, 10, 10, 10, 13, 13, 13, 13, 15, 19, 19, 1] 19 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: 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: REAL250005054020 none CN(CCNC(=O)C1=CN=NN1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 12, 3, 3, 1, 3, 1, 1, 1, 1, 1, 17, 19, 19, 19, 19, 19, 19, 19, 17, 17, 17, 15, 15, 12, 12, 3, 1, 1, 19] 19 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054020 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054020 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054020/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054020/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054020 Building REAL250005054021 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054021' /scratch/stefan/7922901/working/building/REAL250005054021 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054021 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054021/0 /scratch/stefan/7922901/working/building/REAL250005054021 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/132 `/scratch/stefan/7922901/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)NC=N1) `REAL250005054021.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054021 none CC1=C(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 121, 121, 121, 71, 61, 27, 12, 27, 1, 12, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 121, 71, 71, 61, 61, 27, 27, 27, 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: 556 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054021 none CC1=C(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 9, 9, 9, 44, 75, 118, 118, 187, 187, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 9, 43, 43, 75, 75, 118, 118, 118, 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: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054021 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054021 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054021/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054021 Building REAL250005054022 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054022' /scratch/stefan/7922901/working/building/REAL250005054022 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054022 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054022/0 /scratch/stefan/7922901/working/building/REAL250005054022 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/133 `/scratch/stefan/7922901/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054022.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054022 none COCC1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 129, 129, 129, 75, 56, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 198, 198, 201, 201, 201, 201, 201, 129, 75, 75, 56, 56, 17, 17, 17, 1, 198, 198, 198, 198] 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: 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: REAL250005054022 none COCC1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 7, 7, 7, 28, 42, 91, 91, 182, 182, 198, 198, 198, 198, 198, 1, 1, 16, 16, 16, 7, 7, 7, 28, 28, 42, 42, 91, 91, 91, 198, 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: 679 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054022 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054022 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054022/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054022 Building REAL250005054023 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054023' /scratch/stefan/7922901/working/building/REAL250005054023 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054023 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054023/0 /scratch/stefan/7922901/working/building/REAL250005054023 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/134 `/scratch/stefan/7922901/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054023.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054023 none COCC(C)(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 132, 201, 201, 132, 132, 65, 51, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 65, 65, 51, 51, 15, 15, 15, 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: 861 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054023 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054023 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054023/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054023 Building REAL250005054024 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054024' /scratch/stefan/7922901/working/building/REAL250005054024 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054024 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054024/0 /scratch/stefan/7922901/working/building/REAL250005054024 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/135 `/scratch/stefan/7922901/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NN(C)N=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054024.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054024 none CN(CCNC(=O)C1=NN(C)N=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 6, 18, 27, 27, 44, 44, 44, 59, 59, 59, 59, 59, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 27, 27, 27, 27, 44, 59, 59, 59, 59, 1] 59 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: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054024 none CN(CCNC(=O)C1=NN(C)N=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [43, 39, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 43, 59, 59, 59, 59, 59, 59, 59, 43, 43, 43, 39, 39, 28, 28, 8, 2, 2, 2, 1, 59] 59 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054024 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054024 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054024/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054024 Building REAL250005054025 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054025' /scratch/stefan/7922901/working/building/REAL250005054025 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054025 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054025/0 /scratch/stefan/7922901/working/building/REAL250005054025 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/136 `/scratch/stefan/7922901/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCC(F)F)C(=O)C1=CC(=O)[N-]O1) `REAL250005054025.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054025 none CN(CCNC(=O)CCC(F)F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 15, 23, 25, 49, 49, 49, 147, 161, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 23, 23, 25, 25, 49, 147, 147, 193, 193, 177, 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: 1009 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054025 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054025 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054025/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054025 Building REAL250005054026 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054026' /scratch/stefan/7922901/working/building/REAL250005054026 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054026 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054026/0 /scratch/stefan/7922901/working/building/REAL250005054026 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/137 `/scratch/stefan/7922901/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1(C)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054026.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054026 none CN(CCNC(=O)CC1(C)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 33, 38, 70, 70, 70, 183, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 33, 33, 38, 38, 70, 183, 183, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005054026 none CN(CCNC(=O)CC1(C)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 126, 92, 27, 27, 8, 27, 1, 1, 1, 1, 1, 164, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 126, 126, 92, 92, 27, 8, 8, 2, 2, 2, 1, 1, 1, 1, 201] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 815 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054026 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054026 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054026/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054026 Building REAL250005054027 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054027' /scratch/stefan/7922901/working/building/REAL250005054027 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054027 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054027/0 /scratch/stefan/7922901/working/building/REAL250005054027 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/138 `/scratch/stefan/7922901/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(CCF)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054027.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054027 none CN(CCNC(=O)C1(CCF)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 33, 37, 67, 67, 67, 143, 201, 201, 143, 143, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 37, 37, 67, 201, 201, 201, 201, 143, 143, 143, 143, 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: 777 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: REAL250005054027 none CN(CCNC(=O)C1(CCF)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 55, 34, 7, 7, 1, 7, 1, 1, 7, 12, 1, 1, 90, 134, 134, 143, 143, 143, 143, 143, 90, 90, 90, 55, 55, 34, 34, 7, 7, 7, 12, 12, 1, 1, 1, 1, 143] 201 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 11, 12] set([0, 1, 2, 3, 4, 6, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 577 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054027 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054027 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054027/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054027 Building REAL250005054028 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054028' /scratch/stefan/7922901/working/building/REAL250005054028 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054028 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054028/0 /scratch/stefan/7922901/working/building/REAL250005054028 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/139 `/scratch/stefan/7922901/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005054028.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054028 none CCC(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 9, 9, 6, 4, 6, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9, 6, 6, 6, 1, 10, 10, 10, 10, 10, 10] 10 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: 39 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054028 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054028 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054028/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054028 Building REAL250005054029 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054029' /scratch/stefan/7922901/working/building/REAL250005054029 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054029 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054029/0 /scratch/stefan/7922901/working/building/REAL250005054029 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/140 `/scratch/stefan/7922901/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CSN=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054029.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054029 none CN(CCNC(=O)C1=CSN=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 14, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 6, 18, 27, 27, 34, 34, 34, 56, 56, 56, 56, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 27, 27, 27, 27, 34, 56, 1] 56 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: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054029 none CN(CCNC(=O)C1=CSN=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 14, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 36, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 45, 56, 56, 56, 56, 56, 56, 56, 45, 45, 45, 36, 36, 25, 25, 9, 1, 56] 56 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054029 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054029 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054029/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054029 Building REAL250005054030 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054030' /scratch/stefan/7922901/working/building/REAL250005054030 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054030 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054030/0 /scratch/stefan/7922901/working/building/REAL250005054030 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/141 `/scratch/stefan/7922901/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(C)CCCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054030.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054030 none CN(CCNC(=O)C1(C)CCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 23, 51, 60, 94, 94, 94, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 51, 51, 60, 60, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 682 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: REAL250005054030 none CN(CCNC(=O)C1(C)CCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 54, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 87, 182, 182, 201, 201, 201, 201, 201, 87, 87, 87, 54, 54, 26, 26, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40]) total number of confs: 693 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054030 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054030 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054030/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054030 Building REAL250005054031 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054031' /scratch/stefan/7922901/working/building/REAL250005054031 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054031 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054031/0 /scratch/stefan/7922901/working/building/REAL250005054031 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/142 `/scratch/stefan/7922901/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CN=CO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054031.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054031 none CN(CCNC(=O)C1=CN=CO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 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: [16, 6, 16, 37, 41, 63, 63, 63, 111, 111, 111, 111, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 37, 37, 41, 41, 63, 111, 111, 1] 111 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: 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: REAL250005054031 none CN(CCNC(=O)C1=CN=CO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 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: [63, 44, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 63, 109, 109, 111, 111, 111, 111, 111, 63, 63, 63, 44, 44, 25, 25, 7, 1, 1, 111] 111 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054031 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054031 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054031/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054031 Building REAL250005054032 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054032' /scratch/stefan/7922901/working/building/REAL250005054032 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054032 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054032/0 /scratch/stefan/7922901/working/building/REAL250005054032 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/143 `/scratch/stefan/7922901/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1CCC(=O)N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054032.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054032 none CN(CCNC(=O)[C@@H]1CCC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 27, 27, 47, 47, 47, 80, 80, 80, 80, 80, 80, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 47, 80, 80, 80, 80, 80, 1] 80 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: 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: REAL250005054032 none CN(CCNC(=O)[C@@H]1CCC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [65, 58, 43, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 65, 79, 79, 80, 80, 80, 80, 80, 65, 65, 65, 58, 58, 43, 43, 11, 1, 1, 1, 1, 1, 80] 80 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054032 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054032 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054032/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054032 Building REAL250005054033 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054033' /scratch/stefan/7922901/working/building/REAL250005054033 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054033 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054033/0 /scratch/stefan/7922901/working/building/REAL250005054033 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/144 `/scratch/stefan/7922901/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@H+](C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054033.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054033 none CCC[N@H+](C)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 14, 16, 16, 13, 13, 13, 7, 7, 7, 6, 7, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 14, 14, 13, 7, 7, 7, 7, 7, 7, 7, 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: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054033 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054033/1 /scratch/stefan/7922901/working/building/REAL250005054033 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/145 `/scratch/stefan/7922901/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@@H+](C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054033.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005054033 none CCC[N@@H+](C)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 14, 16, 16, 13, 13, 13, 7, 7, 7, 6, 7, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 14, 14, 13, 7, 7, 7, 7, 7, 7, 7, 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: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054033 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054033 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054033/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054033/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054033 Building REAL250005054034 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054034' /scratch/stefan/7922901/working/building/REAL250005054034 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054034 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054034/0 /scratch/stefan/7922901/working/building/REAL250005054034 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/146 `/scratch/stefan/7922901/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC=C1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054034.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054034 none CC1=NNC=C1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 95, 95, 95, 95, 65, 51, 20, 10, 20, 1, 10, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 65, 65, 51, 51, 20, 20, 20, 1] 95 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: 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: REAL250005054034 none CC1=NNC=C1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 4, 4, 4, 20, 33, 53, 53, 85, 85, 95, 95, 95, 95, 95, 2, 2, 2, 1, 1, 4, 20, 20, 33, 33, 53, 53, 53, 95] 95 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: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054034 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054034 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054034/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054034 Building REAL250005054035 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054035' /scratch/stefan/7922901/working/building/REAL250005054035 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054035 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054035/0 /scratch/stefan/7922901/working/building/REAL250005054035 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/147 `/scratch/stefan/7922901/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)NN=N1) `REAL250005054035.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054035 none CC1=C(C(=O)NCCN(C)C(=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.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 129, 129, 129, 74, 60, 24, 10, 24, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 129, 74, 74, 60, 60, 24, 24, 24, 1, 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]) total number of confs: 572 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: REAL250005054035 none CC1=C(C(=O)NCCN(C)C(=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.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 11, 11, 11, 45, 74, 106, 106, 195, 195, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 11, 45, 45, 74, 74, 106, 106, 106, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 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: 750 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054035 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054035/1 /scratch/stefan/7922901/working/building/REAL250005054035 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/148 `/scratch/stefan/7922901/working/3D/148' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNN=C1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054035.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054035 none CC1=NNN=C1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 194, 194, 194, 91, 59, 24, 10, 24, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 194, 91, 91, 59, 59, 24, 24, 24, 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: 711 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: REAL250005054035 none CC1=NNN=C1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 23, 48, 89, 89, 168, 168, 201, 201, 201, 201, 201, 2, 2, 2, 1, 3, 23, 23, 48, 48, 89, 89, 89, 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: 664 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054035 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054035 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054035/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054035/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054035 Building REAL250005054036 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054036' /scratch/stefan/7922901/working/building/REAL250005054036 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054036 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054036/0 /scratch/stefan/7922901/working/building/REAL250005054036 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/149 `/scratch/stefan/7922901/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(OC)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054036.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054036 none CCCC(OC)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 148, 113, 148, 150, 113, 113, 67, 48, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 148, 150, 150, 150, 113, 67, 67, 48, 48, 18, 18, 18, 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: 951 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054036 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054036 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054036/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054036 Building REAL250005054037 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054037' /scratch/stefan/7922901/working/building/REAL250005054037 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054037 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054037/0 /scratch/stefan/7922901/working/building/REAL250005054037 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/150 `/scratch/stefan/7922901/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C(C)(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054037.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054037 none C=C(C)C(C)(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 138, 201, 201, 138, 138, 72, 60, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 72, 72, 60, 60, 22, 22, 22, 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: 800 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054037 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054037 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054037/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054037 Building REAL250005054038 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054038' /scratch/stefan/7922901/working/building/REAL250005054038 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054038 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054038/0 /scratch/stefan/7922901/working/building/REAL250005054038 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/151 `/scratch/stefan/7922901/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(N)=O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054038.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054038 none CC(CC(N)=O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [79, 74, 79, 79, 80, 80, 74, 74, 51, 38, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 79, 80, 80, 74, 51, 51, 38, 38, 14, 14, 14, 1] 80 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: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054038 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054038 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054038/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054038 Building REAL250005054039 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054039' /scratch/stefan/7922901/working/building/REAL250005054039 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054039 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054039/0 /scratch/stefan/7922901/working/building/REAL250005054039 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/152 `/scratch/stefan/7922901/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCNC1=O)C(=O)C1=CC(=O)[N-]O1) `REAL250005054039.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054039 none CN(CCNC(=O)C1CCNC1=O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [26, 10, 26, 49, 57, 112, 112, 112, 155, 155, 155, 155, 155, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 49, 49, 57, 57, 112, 155, 155, 155, 155, 155, 155, 1] 155 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: 529 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: REAL250005054039 none CN(CCNC(=O)C1CCNC1=O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 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 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [102, 73, 45, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 102, 147, 147, 155, 155, 155, 155, 155, 102, 102, 102, 73, 73, 45, 45, 10, 1, 1, 1, 1, 1, 1, 155] 155 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 602 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054039 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054039 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054039/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054039 Building REAL250005054040 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054040' /scratch/stefan/7922901/working/building/REAL250005054040 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054040 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054040/0 /scratch/stefan/7922901/working/building/REAL250005054040 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/153 `/scratch/stefan/7922901/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054040.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054040 none C=CC(C)(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 201, 201, 129, 129, 67, 55, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 67, 67, 55, 55, 19, 19, 19, 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: 819 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054040 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054040 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054040/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054040 Building REAL250005054041 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054041' /scratch/stefan/7922901/working/building/REAL250005054041 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005054041 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054041/0 /scratch/stefan/7922901/working/building/REAL250005054041 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/154 `/scratch/stefan/7922901/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1CCC[N@@H+]1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054041.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054041 none CN(CCNC(=O)[C@H]1CCC[N@@H+]1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 5 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: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054041 none CN(CCNC(=O)[C@H]1CCC[N@@H+]1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5] 5 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054041 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054041/1 /scratch/stefan/7922901/working/building/REAL250005054041 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/155 `/scratch/stefan/7922901/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1CCC[N@H+]1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054041.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054041/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054041 none CN(CCNC(=O)[C@H]1CCC[N@H+]1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 8, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 12 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: 35 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: REAL250005054041 none CN(CCNC(=O)[C@H]1CCC[N@H+]1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 11, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 8, 8, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12] 12 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40]) total number of confs: 56 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054041 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `2' /scratch/stefan/7922901/working/building/REAL250005054041/2 /scratch/stefan/7922901/working/building/REAL250005054041 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 2 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/156 `/scratch/stefan/7922901/working/3D/156' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1CCCN1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054041.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005054041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054041/2/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: REAL250005054041 none CN(CCNC(=O)[C@H]1CCCN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 9, 21, 30, 30, 56, 56, 56, 92, 92, 92, 92, 92, 92, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 30, 30, 30, 30, 56, 92, 92, 92, 92, 92, 92, 92, 92, 92, 1] 92 rigid atoms, others: [39, 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]) total number of confs: 309 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054041 none CN(CCNC(=O)[C@H]1CCCN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [77, 63, 43, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 77, 92, 92, 92, 92, 92, 92, 92, 77, 77, 77, 63, 63, 43, 43, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 92] 92 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39]) total number of confs: 380 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054041 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054041 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054041/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054041/1.* 2: /scratch/stefan/7922901/working/building/REAL250005054041/2.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054041 Building REAL250005054042 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054042' /scratch/stefan/7922901/working/building/REAL250005054042 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054042 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054042/0 /scratch/stefan/7922901/working/building/REAL250005054042 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/157 `/scratch/stefan/7922901/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054042.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054042 none C[C@@H]1C[C@H]1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 201, 99, 99, 64, 49, 17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 99, 64, 64, 49, 49, 17, 17, 17, 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: 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: REAL250005054042 none C[C@@H]1C[C@H]1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 73, 115, 115, 188, 188, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 12, 44, 44, 73, 73, 115, 115, 115, 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: 736 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054042 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054042 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054042/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054042 Building REAL250005054043 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054043' /scratch/stefan/7922901/working/building/REAL250005054043 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054043 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054043/0 /scratch/stefan/7922901/working/building/REAL250005054043 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/158 `/scratch/stefan/7922901/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(C)CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054043.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054043 none CN(CCNC(=O)C1(C)CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 47, 59, 74, 74, 74, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 47, 47, 59, 59, 74, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 619 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: REAL250005054043 none CN(CCNC(=O)C1(C)CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 63, 34, 7, 7, 1, 7, 1, 1, 1, 1, 1, 104, 190, 190, 201, 201, 201, 201, 201, 104, 104, 104, 63, 63, 34, 34, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 740 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054043 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054043 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054043/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054043 Building REAL250005054044 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054044' /scratch/stefan/7922901/working/building/REAL250005054044 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054044 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054044/0 /scratch/stefan/7922901/working/building/REAL250005054044 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/159 `/scratch/stefan/7922901/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1COC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054044.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054044 none CC1COC(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 154, 154, 85, 52, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 154, 85, 85, 52, 52, 19, 19, 19, 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: 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: REAL250005054044 none CC1COC(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 78, 118, 118, 190, 190, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 11, 47, 47, 78, 78, 118, 118, 118, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 24, 25, 26, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054044 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054044 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054044/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054044 Building REAL250005054045 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054045' /scratch/stefan/7922901/working/building/REAL250005054045 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054045 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054045/0 /scratch/stefan/7922901/working/building/REAL250005054045 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/160 `/scratch/stefan/7922901/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]12C[C@H]1CCC2)C(=O)C1=CC(=O)[N-]O1) `REAL250005054045.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054045 none CN(CCNC(=O)[C@]12C[C@H]1CCC2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 48, 60, 81, 81, 81, 201, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 48, 48, 60, 60, 81, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 470 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: REAL250005054045 none CN(CCNC(=O)[C@]12C[C@H]1CCC2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 63, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 107, 188, 188, 201, 201, 201, 201, 201, 107, 107, 107, 63, 63, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38]) total number of confs: 724 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054045 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054045 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054045/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054045 Building REAL250005054046 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054046' /scratch/stefan/7922901/working/building/REAL250005054046 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054046 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054046/0 /scratch/stefan/7922901/working/building/REAL250005054046 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/161 `/scratch/stefan/7922901/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054046.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054046 none CC[NH+](CC)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 10, 10, 10, 11, 10, 10, 10, 6, 6, 6, 5, 6, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 1] 12 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: 39 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054046 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054046 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054046/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054046 Building REAL250005054047 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054047' /scratch/stefan/7922901/working/building/REAL250005054047 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054047 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054047/0 /scratch/stefan/7922901/working/building/REAL250005054047 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/162 `/scratch/stefan/7922901/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054047.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054047 none CCC(F)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 110, 173, 110, 110, 59, 42, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 173, 110, 59, 59, 42, 42, 18, 18, 18, 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: 870 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054047 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054047 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054047/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054047 Building REAL250005054048 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054048' /scratch/stefan/7922901/working/building/REAL250005054048 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054048 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054048/0 /scratch/stefan/7922901/working/building/REAL250005054048 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/163 `/scratch/stefan/7922901/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCCF)C(=O)C1=CC(=O)[N-]O1) `REAL250005054048.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054048 none CN(CCNC(=O)CCCF)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 22, 22, 56, 56, 56, 172, 196, 201, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 22, 22, 22, 22, 56, 172, 172, 201, 201, 201, 201, 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: 821 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054048 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054048 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054048/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054048 Building REAL250005054049 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054049' /scratch/stefan/7922901/working/building/REAL250005054049 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054049 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054049/0 /scratch/stefan/7922901/working/building/REAL250005054049 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/164 `/scratch/stefan/7922901/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC=C1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054049.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054049 none CC1=COC=C1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 198, 198, 198, 155, 155, 155, 92, 64, 26, 10, 26, 1, 10, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 198, 155, 92, 92, 64, 64, 26, 26, 26, 1] 198 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: 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: REAL250005054049 none CC1=COC=C1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 11, 44, 75, 112, 112, 180, 180, 198, 198, 198, 198, 198, 2, 2, 2, 1, 1, 11, 44, 44, 75, 75, 112, 112, 112, 198] 198 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: 713 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054049 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054049 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054049/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054049 Building REAL250005054050 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054050' /scratch/stefan/7922901/working/building/REAL250005054050 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054050 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054050/0 /scratch/stefan/7922901/working/building/REAL250005054050 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/165 `/scratch/stefan/7922901/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054050.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054050 none C[C@H]1C[C@@H]1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 98, 201, 98, 98, 63, 48, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 98, 63, 63, 48, 48, 16, 16, 16, 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: 693 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054050 none C[C@H]1C[C@@H]1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 74, 116, 116, 189, 189, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 12, 45, 45, 74, 74, 116, 116, 116, 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: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054050 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054050 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054050/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054050 Building REAL250005054051 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054051' /scratch/stefan/7922901/working/building/REAL250005054051 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054051 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054051/0 /scratch/stefan/7922901/working/building/REAL250005054051 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/166 `/scratch/stefan/7922901/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(C)C=CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054051.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054051 none CN(CCNC(=O)C1(C)C=CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 9, 21, 40, 43, 68, 68, 68, 125, 125, 125, 125, 125, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 40, 40, 43, 43, 68, 125, 125, 125, 125, 125, 125, 125, 125, 125, 1] 125 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: 421 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054051 none CN(CCNC(=O)C1(C)C=CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [76, 51, 29, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 76, 121, 121, 125, 125, 125, 125, 125, 76, 76, 76, 51, 51, 29, 29, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 125] 125 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 479 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054051 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054051 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054051/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054051 Building REAL250005054052 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054052' /scratch/stefan/7922901/working/building/REAL250005054052 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054052 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054052/0 /scratch/stefan/7922901/working/building/REAL250005054052 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/167 `/scratch/stefan/7922901/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NN(C)N=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054052.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054052 none CN(CCNC(=O)C1=NN(C)N=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'N.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', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 16, 17, 17, 30, 30, 30, 38, 38, 38, 38, 38, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 17, 17, 17, 17, 30, 38, 38, 38, 1] 38 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: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054052 none CN(CCNC(=O)C1=NN(C)N=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'N.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', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 5, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [32, 28, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 32, 38, 38, 38, 38, 38, 38, 38, 32, 32, 32, 28, 28, 24, 24, 8, 2, 2, 2, 38] 38 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054052 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054052 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054052/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054052 Building REAL250005054053 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054053' /scratch/stefan/7922901/working/building/REAL250005054053 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054053 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054053/0 /scratch/stefan/7922901/working/building/REAL250005054053 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/168 `/scratch/stefan/7922901/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(F)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054053.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054053 none CC(C)C(F)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 166, 201, 103, 166, 103, 103, 62, 40, 18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 166, 103, 62, 62, 40, 40, 18, 18, 18, 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: 867 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054053 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054053 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054053/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054053 Building REAL250005054054 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054054' /scratch/stefan/7922901/working/building/REAL250005054054 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054054 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054054/0 /scratch/stefan/7922901/working/building/REAL250005054054 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/169 `/scratch/stefan/7922901/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)C(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054054.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054054 none C=CC(C)C(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 65, 89, 65, 65, 44, 37, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 65, 44, 44, 37, 37, 15, 15, 15, 1] 89 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054054 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054054 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054054/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054054 Building REAL250005054055 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054055' /scratch/stefan/7922901/working/building/REAL250005054055 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054055 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054055/0 /scratch/stefan/7922901/working/building/REAL250005054055 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/170 `/scratch/stefan/7922901/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005054055.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054055 none CCC1(C(=O)NCCN(C)C(=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.3', '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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 118, 118, 118, 74, 63, 21, 10, 21, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 118, 74, 74, 63, 63, 21, 21, 21, 1, 201, 201, 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, 39, 40]) total number of confs: 737 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: REAL250005054055 none CCC1(C(=O)NCCN(C)C(=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.3', '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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 24, 44, 85, 85, 171, 171, 201, 201, 201, 201, 201, 1, 1, 1, 3, 3, 3, 3, 3, 5, 24, 24, 44, 44, 85, 85, 85, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 36, 37, 35, 39, 40, 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: 647 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054055 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054055 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054055/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054055 Building REAL250005054056 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054056' /scratch/stefan/7922901/working/building/REAL250005054056 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054056 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054056/0 /scratch/stefan/7922901/working/building/REAL250005054056 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/171 `/scratch/stefan/7922901/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054056.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054056 none CC#CCCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 149, 135, 53, 53, 53, 46, 38, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 190, 192, 173, 173, 135, 135, 53, 46, 46, 38, 38, 16, 16, 16, 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: 1036 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054056 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054056 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054056/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054056 Building REAL250005054057 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054057' /scratch/stefan/7922901/working/building/REAL250005054057 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054057 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054057/0 /scratch/stefan/7922901/working/building/REAL250005054057 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/172 `/scratch/stefan/7922901/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1[C@@H]2COC[C@@H]21)C(=O)C1=CC(=O)[N-]O1) `REAL250005054057.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054057 none CN(CCNC(=O)[C@H]1[C@@H]2COC[C@@H]21)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.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, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [24, 8, 24, 50, 58, 97, 97, 97, 201, 201, 201, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 50, 50, 58, 58, 97, 201, 201, 201, 201, 1] 201 rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 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: REAL250005054057 none CN(CCNC(=O)[C@H]1[C@@H]2COC[C@@H]21)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.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, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [138, 102, 70, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 138, 191, 191, 201, 201, 201, 201, 201, 138, 138, 138, 102, 102, 70, 70, 13, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 766 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054057 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054057 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054057/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054057 Building REAL250005054058 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054058' /scratch/stefan/7922901/working/building/REAL250005054058 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054058 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054058/0 /scratch/stefan/7922901/working/building/REAL250005054058 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/173 `/scratch/stefan/7922901/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCCC1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054058.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054058 none CN(CCNC(=O)CCCC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 13, 20, 20, 23, 23, 23, 90, 100, 137, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 20, 20, 20, 20, 23, 90, 90, 123, 123, 139, 139, 201, 201, 201, 201, 201, 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: 984 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054058 none CN(CCNC(=O)CCCC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 158, 119, 57, 57, 11, 57, 7, 3, 1, 1, 1, 1, 178, 197, 197, 201, 201, 201, 201, 201, 178, 178, 178, 158, 158, 119, 119, 57, 11, 11, 7, 7, 3, 3, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40]) total number of confs: 847 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054058 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054058 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054058/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054058 Building REAL250005054059 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054059' /scratch/stefan/7922901/working/building/REAL250005054059 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054059 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054059/0 /scratch/stefan/7922901/working/building/REAL250005054059 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/174 `/scratch/stefan/7922901/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCC1(C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054059.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054059 none CN(CCNC(=O)C1CCC1(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 10, 23, 54, 67, 110, 110, 110, 126, 126, 126, 126, 126, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 54, 54, 67, 67, 110, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 1] 126 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: 467 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: REAL250005054059 none CN(CCNC(=O)C1CCC1(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [67, 46, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 67, 114, 114, 126, 126, 126, 126, 126, 67, 67, 67, 46, 46, 30, 30, 7, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 126] 126 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 454 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054059 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054059 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054059/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054059 Building REAL250005054060 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054060' /scratch/stefan/7922901/working/building/REAL250005054060 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054060 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054060/0 /scratch/stefan/7922901/working/building/REAL250005054060 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/175 `/scratch/stefan/7922901/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005054060.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054060 none CC1=COC(C(=O)NCCN(C)C(=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.3', '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, 12, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 191, 191, 191, 111, 84, 32, 12, 32, 1, 12, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 111, 111, 84, 84, 32, 32, 32, 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: 715 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: REAL250005054060 none CC1=COC(C(=O)NCCN(C)C(=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.3', '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, 12, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 6, 6, 6, 29, 52, 98, 98, 176, 176, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 6, 28, 28, 52, 52, 98, 98, 98, 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: 665 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054060 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054060 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054060/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054060 Building REAL250005054061 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054061' /scratch/stefan/7922901/working/building/REAL250005054061 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054061 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054061/0 /scratch/stefan/7922901/working/building/REAL250005054061 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/176 `/scratch/stefan/7922901/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(CC)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054061.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054061 none C=CC(CC)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 79, 70, 79, 80, 38, 38, 38, 34, 31, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 80, 80, 80, 79, 80, 80, 80, 80, 80, 70, 70, 38, 34, 34, 31, 31, 15, 15, 15, 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: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054061 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054061 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054061/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054061 Building REAL250005054062 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054062' /scratch/stefan/7922901/working/building/REAL250005054062 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054062 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054062/0 /scratch/stefan/7922901/working/building/REAL250005054062 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/177 `/scratch/stefan/7922901/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(C)(C)C1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054062.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054062 none CN(CCNC(=O)C(C)(C)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 31, 33, 60, 60, 60, 125, 126, 126, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 31, 31, 33, 33, 60, 126, 126, 126, 126, 126, 126, 201, 201, 201, 201, 201, 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: 826 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054062 none CN(CCNC(=O)C(C)(C)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 106, 70, 24, 24, 9, 24, 1, 9, 9, 1, 1, 1, 138, 198, 198, 201, 201, 201, 201, 201, 138, 138, 138, 106, 106, 70, 70, 24, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [35, 36, 37, 38, 7, 10, 11, 12, 39] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40]) total number of confs: 797 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054062 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054062 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054062/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054062 Building REAL250005054063 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054063' /scratch/stefan/7922901/working/building/REAL250005054063 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054063 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054063/0 /scratch/stefan/7922901/working/building/REAL250005054063 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/178 `/scratch/stefan/7922901/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1C[C@H]2C[C@H]2C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054063.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054063 none CN(CCNC(=O)[C@H]1C[C@H]2C[C@H]2C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 54, 68, 110, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 54, 54, 68, 68, 110, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 680 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054063 none CN(CCNC(=O)[C@H]1C[C@H]2C[C@H]2C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 80, 52, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 195, 195, 201, 201, 201, 201, 201, 126, 126, 126, 80, 80, 52, 52, 9, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 37] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054063 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054063 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054063/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054063 Building REAL250005054064 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054064' /scratch/stefan/7922901/working/building/REAL250005054064 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054064 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054064/0 /scratch/stefan/7922901/working/building/REAL250005054064 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/179 `/scratch/stefan/7922901/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1=CON=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054064.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054064 none CN(CCNC(=O)CC1=CON=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 12, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 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: [16, 6, 16, 23, 23, 51, 51, 51, 94, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 23, 23, 23, 23, 51, 94, 94, 201, 201, 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: 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: REAL250005054064 none CN(CCNC(=O)CC1=CON=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 12, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 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: [166, 122, 81, 15, 15, 4, 15, 1, 1, 1, 1, 1, 1, 166, 201, 201, 201, 201, 201, 201, 201, 166, 166, 166, 122, 122, 81, 81, 15, 4, 4, 1, 1, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 835 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054064 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054064 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054064/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054064 Building REAL250005054065 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054065' /scratch/stefan/7922901/working/building/REAL250005054065 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054065 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054065/0 /scratch/stefan/7922901/working/building/REAL250005054065 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/180 `/scratch/stefan/7922901/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCC(C)(C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054065.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054065 none CN(CCNC(=O)CCC(C)(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 45, 55, 86, 86, 86, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 21, 21, 21, 45, 45, 55, 55, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 830 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054065 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054065 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054065/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054065 Building REAL250005054066 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054066' /scratch/stefan/7922901/working/building/REAL250005054066 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054066 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054066/0 /scratch/stefan/7922901/working/building/REAL250005054066 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/181 `/scratch/stefan/7922901/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC=NC=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054066.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054066 none CN(CCNC(=O)C1=CC=NC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 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: [21, 8, 21, 28, 28, 44, 44, 44, 59, 59, 59, 59, 59, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 28, 28, 28, 28, 44, 59, 59, 59, 1] 59 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: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054066 none CN(CCNC(=O)C1=CC=NC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [52, 39, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 52, 59, 59, 59, 59, 59, 59, 59, 52, 52, 52, 39, 39, 27, 27, 9, 1, 1, 1, 59] 59 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054066 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054066 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054066/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054066 Building REAL250005054067 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054067' /scratch/stefan/7922901/working/building/REAL250005054067 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054067 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054067/0 /scratch/stefan/7922901/working/building/REAL250005054067 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/182 `/scratch/stefan/7922901/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1=CC=CO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054067.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054067 none CN(CCNC(=O)CC1=CC=CO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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: [15, 6, 15, 21, 21, 41, 41, 41, 151, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 21, 21, 21, 21, 41, 151, 151, 201, 201, 201, 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: 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: REAL250005054067 none CN(CCNC(=O)CC1=CC=CO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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: [169, 141, 111, 35, 35, 5, 35, 1, 1, 1, 1, 1, 1, 169, 201, 201, 201, 201, 201, 201, 201, 169, 169, 169, 141, 141, 111, 111, 35, 5, 5, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/7922901/working/building/REAL250005054067 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054067 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054067/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054067 Building REAL250005054068 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054068' /scratch/stefan/7922901/working/building/REAL250005054068 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054068 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054068/0 /scratch/stefan/7922901/working/building/REAL250005054068 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/183 `/scratch/stefan/7922901/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NC=CC=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054068.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054068 none CN(CCNC(=O)C1=NC=CC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', '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, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 13, 13, 19, 19, 19, 21, 21, 19, 21, 21, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 13, 13, 13, 13, 19, 21, 19, 21, 1] 21 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: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054068 none CN(CCNC(=O)C1=NC=CC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', '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, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 21, 21, 21, 21, 21, 21, 21, 19, 19, 19, 17, 17, 13, 13, 6, 1, 1, 1, 21] 21 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054068 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054068 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054068/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054068 Building REAL250005054069 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054069' /scratch/stefan/7922901/working/building/REAL250005054069 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054069 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054069/0 /scratch/stefan/7922901/working/building/REAL250005054069 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/184 `/scratch/stefan/7922901/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054069.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054069 none CCC(C)CCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 119, 201, 117, 47, 47, 47, 39, 33, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126, 119, 119, 47, 39, 39, 33, 33, 16, 16, 16, 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: 1017 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054069 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054069 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054069/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054069 Building REAL250005054070 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054070' /scratch/stefan/7922901/working/building/REAL250005054070 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054070 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054070/0 /scratch/stefan/7922901/working/building/REAL250005054070 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/185 `/scratch/stefan/7922901/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC=CN=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054070.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054070 none CN(CCNC(=O)C1=CC=CN=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 6, 7, 7, 7, 3, 7, 3, 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: [14, 6, 14, 21, 21, 37, 37, 37, 61, 61, 61, 61, 61, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 21, 21, 21, 21, 37, 61, 61, 61, 1] 61 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: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054070 none CN(CCNC(=O)C1=CC=CN=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 6, 7, 7, 7, 3, 7, 3, 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: [52, 38, 30, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 52, 61, 61, 61, 61, 61, 61, 61, 52, 52, 52, 38, 38, 30, 30, 10, 1, 1, 1, 61] 61 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054070 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054070 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054070/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054070 Building REAL250005054071 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054071' /scratch/stefan/7922901/working/building/REAL250005054071 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054071 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054071/0 /scratch/stefan/7922901/working/building/REAL250005054071 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/186 `/scratch/stefan/7922901/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OCCC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054071.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054071 none CC1OCCC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 97, 91, 91, 91, 64, 50, 22, 10, 22, 1, 10, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97, 97, 97, 97, 91, 64, 64, 50, 50, 22, 22, 22, 1] 97 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: 389 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: REAL250005054071 none CC1OCCC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 22, 43, 43, 87, 87, 97, 97, 97, 97, 97, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 13, 13, 22, 22, 43, 43, 43, 97] 97 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: 321 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054071 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054071 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054071/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054071 Building REAL250005054072 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054072' /scratch/stefan/7922901/working/building/REAL250005054072 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054072 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054072/0 /scratch/stefan/7922901/working/building/REAL250005054072 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/187 `/scratch/stefan/7922901/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(C)CCOC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054072.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054072 none CN(CCNC(=O)C1(C)CCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [26, 10, 26, 55, 65, 106, 106, 106, 186, 186, 186, 186, 186, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 55, 55, 65, 65, 106, 186, 186, 186, 186, 186, 186, 186, 186, 186, 1] 186 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: 635 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: REAL250005054072 none CN(CCNC(=O)C1(C)CCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [93, 54, 28, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 93, 168, 168, 186, 186, 186, 186, 186, 93, 93, 93, 54, 54, 28, 28, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 186] 186 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 654 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054072 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054072 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054072/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054072 Building REAL250005054073 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054073' /scratch/stefan/7922901/working/building/REAL250005054073 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054073 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054073/0 /scratch/stefan/7922901/working/building/REAL250005054073 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/188 `/scratch/stefan/7922901/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054073.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054073 none CCC(CC)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 201, 201, 63, 63, 63, 57, 39, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 63, 57, 57, 39, 39, 16, 16, 16, 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: 861 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054073 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054073 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054073/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054073 Building REAL250005054074 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054074' /scratch/stefan/7922901/working/building/REAL250005054074 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054074 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054074/0 /scratch/stefan/7922901/working/building/REAL250005054074 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/189 `/scratch/stefan/7922901/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054074.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054074 none CCC(C)C(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 103, 104, 71, 103, 71, 71, 47, 39, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 104, 104, 104, 104, 103, 103, 103, 103, 71, 47, 47, 39, 39, 15, 15, 15, 1] 104 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: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054074 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054074 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054074/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054074 Building REAL250005054075 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054075' /scratch/stefan/7922901/working/building/REAL250005054075 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054075 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054075/0 /scratch/stefan/7922901/working/building/REAL250005054075 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/190 `/scratch/stefan/7922901/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054075.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054075 none CCCC(CC)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [167, 167, 143, 86, 143, 144, 86, 86, 46, 38, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 167, 167, 143, 148, 148, 148, 148, 148, 86, 46, 46, 38, 38, 15, 15, 15, 1] 169 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: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054075 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054075 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054075/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054075 Building REAL250005054076 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054076' /scratch/stefan/7922901/working/building/REAL250005054076 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054076 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054076/0 /scratch/stefan/7922901/working/building/REAL250005054076 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/191 `/scratch/stefan/7922901/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCC(F)C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054076.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054076 none CN(CCNC(=O)C1CCC(F)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 27, 58, 68, 110, 110, 110, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 58, 58, 68, 68, 110, 201, 201, 201, 201, 201, 201, 201, 201, 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: 687 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: REAL250005054076 none CN(CCNC(=O)C1CCC(F)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 79, 46, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 121, 189, 189, 201, 201, 201, 201, 201, 121, 121, 121, 79, 79, 46, 46, 9, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 753 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054076 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054076 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054076/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054076 Building REAL250005054077 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054077' /scratch/stefan/7922901/working/building/REAL250005054077 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054077 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054077/0 /scratch/stefan/7922901/working/building/REAL250005054077 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/192 `/scratch/stefan/7922901/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054077.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054077 none C=CCCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 116, 112, 27, 27, 27, 27, 23, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 160, 160, 160, 155, 155, 132, 132, 114, 114, 27, 27, 27, 23, 23, 11, 11, 11, 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: 777 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054077 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054077 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054077/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054077 Building REAL250005054078 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054078' /scratch/stefan/7922901/working/building/REAL250005054078 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054078 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054078/0 /scratch/stefan/7922901/working/building/REAL250005054078 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/193 `/scratch/stefan/7922901/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054078.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054078 none CCC(C)(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 191, 105, 191, 191, 105, 105, 61, 53, 21, 10, 21, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 191, 191, 191, 191, 105, 61, 61, 53, 53, 21, 21, 21, 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: 949 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054078 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054078 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054078/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054078 Building REAL250005054079 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054079' /scratch/stefan/7922901/working/building/REAL250005054079 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054079 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054079/0 /scratch/stefan/7922901/working/building/REAL250005054079 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/194 `/scratch/stefan/7922901/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054079.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054079 none CCCC(C)(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 117, 103, 65, 103, 103, 65, 65, 47, 41, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 121, 121, 103, 103, 103, 103, 103, 103, 65, 47, 47, 41, 41, 16, 16, 16, 1] 121 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: 571 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054079 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054079 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054079/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054079 Building REAL250005054080 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054080' /scratch/stefan/7922901/working/building/REAL250005054080 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054080 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054080/0 /scratch/stefan/7922901/working/building/REAL250005054080 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/195 `/scratch/stefan/7922901/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(C(N)=O)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054080.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054080 none CN(CCNC(=O)C1(C(N)=O)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 20, 20, 38, 38, 38, 50, 50, 50, 50, 50, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 20, 20, 20, 20, 38, 50, 50, 50, 50, 50, 50, 1] 50 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: 175 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: REAL250005054080 none CN(CCNC(=O)C1(C(N)=O)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 8, 11, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 6, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 27, 19, 5, 5, 1, 5, 1, 1, 6, 6, 1, 1, 36, 46, 46, 50, 50, 50, 50, 50, 36, 36, 36, 27, 27, 19, 19, 5, 6, 6, 1, 1, 1, 1, 50] 50 rigid atoms, others: [32, 33, 34, 5, 7, 8, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 207 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054080 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054080 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054080/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054080 Building REAL250005054081 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054081' /scratch/stefan/7922901/working/building/REAL250005054081 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054081 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054081/0 /scratch/stefan/7922901/working/building/REAL250005054081 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/196 `/scratch/stefan/7922901/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(N)=O)C(=O)C1=CC(=O)[N-]O1) `REAL250005054081.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054081 none CN(CCNC(=O)C(N)=O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.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: [5, 8, 5, 5, 8, 1, 11, 1, 8, 11, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 12, 12, 12, 12, 12, 16, 16, 1, 9, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 12, 12, 12, 16, 16, 1] 16 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: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054081 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054081 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054081/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054081 Building REAL250005054082 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054082' /scratch/stefan/7922901/working/building/REAL250005054082 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054082 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054082/0 /scratch/stefan/7922901/working/building/REAL250005054082 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/197 `/scratch/stefan/7922901/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC=C1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054082.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054082 none CC1=NOC=C1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 170, 153, 153, 153, 98, 68, 24, 10, 24, 1, 10, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 153, 98, 98, 68, 68, 24, 24, 24, 1] 170 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: 616 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054082 none CC1=NOC=C1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 1, 8, 8, 8, 36, 61, 91, 91, 148, 148, 170, 170, 170, 170, 170, 2, 2, 2, 1, 8, 35, 35, 61, 61, 91, 91, 91, 170] 170 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: 589 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054082 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054082 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054082/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054082 Building REAL250005054083 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054083' /scratch/stefan/7922901/working/building/REAL250005054083 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054083 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054083/0 /scratch/stefan/7922901/working/building/REAL250005054083 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/198 `/scratch/stefan/7922901/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)CC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054083.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054083 none CCC1(C)CC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 139, 139, 139, 78, 60, 22, 9, 22, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 194, 194, 194, 194, 194, 194, 139, 78, 78, 60, 60, 22, 22, 22, 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: 755 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: REAL250005054083 none CCC1(C)CC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 36, 62, 99, 99, 172, 172, 194, 194, 194, 194, 194, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 6, 36, 36, 62, 62, 99, 99, 99, 194] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 690 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054083 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054083 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054083/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054083 Building REAL250005054084 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054084' /scratch/stefan/7922901/working/building/REAL250005054084 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054084 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054084/0 /scratch/stefan/7922901/working/building/REAL250005054084 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/199 `/scratch/stefan/7922901/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054084.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054084 none COCC(C)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 75, 75, 75, 51, 51, 51, 45, 31, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 75, 75, 75, 75, 75, 75, 51, 45, 45, 31, 31, 16, 16, 16, 1] 86 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: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054084 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054084 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054084/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054084 Building REAL250005054085 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054085' /scratch/stefan/7922901/working/building/REAL250005054085 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054085 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054085/0 /scratch/stefan/7922901/working/building/REAL250005054085 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/200 `/scratch/stefan/7922901/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCC1(C)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054085.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054085 none CN(CCNC(=O)CCC1(C)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 15, 27, 31, 52, 52, 52, 153, 155, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 27, 27, 31, 31, 52, 153, 153, 159, 159, 201, 201, 201, 201, 201, 201, 201, 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: 806 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: REAL250005054085 none CN(CCNC(=O)CCC1(C)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 141, 107, 36, 36, 7, 36, 5, 1, 1, 1, 1, 1, 174, 200, 200, 201, 201, 201, 201, 201, 175, 175, 175, 142, 142, 109, 109, 36, 7, 7, 5, 5, 2, 2, 2, 1, 1, 1, 1, 201] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40]) total number of confs: 841 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054085 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054085 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054085/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054085 Building REAL250005054086 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054086' /scratch/stefan/7922901/working/building/REAL250005054086 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054086 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054086/0 /scratch/stefan/7922901/working/building/REAL250005054086 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/201 `/scratch/stefan/7922901/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)ON=C1) `REAL250005054086.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054086 none CC1=C(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 201, 183, 183, 183, 96, 62, 25, 10, 25, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 183, 96, 96, 62, 62, 25, 25, 25, 1, 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]) total number of confs: 691 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: REAL250005054086 none CC1=C(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 8, 8, 8, 34, 57, 102, 102, 182, 182, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 8, 34, 34, 57, 57, 102, 102, 102, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 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: 700 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054086 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054086 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054086/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054086 Building REAL250005054087 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054087' /scratch/stefan/7922901/working/building/REAL250005054087 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054087 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054087/0 /scratch/stefan/7922901/working/building/REAL250005054087 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/202 `/scratch/stefan/7922901/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(C)CC=CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054087.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054087 none CN(CCNC(=O)C1(C)CC=CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 57, 69, 111, 111, 111, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 27, 27, 27, 57, 57, 69, 69, 111, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 679 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: REAL250005054087 none CN(CCNC(=O)C1(C)CC=CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 53, 28, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 97, 185, 185, 201, 201, 201, 201, 201, 97, 97, 97, 53, 53, 28, 28, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 690 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054087 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054087 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054087/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054087 Building REAL250005054088 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054088' /scratch/stefan/7922901/working/building/REAL250005054088 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054088 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054088/0 /scratch/stefan/7922901/working/building/REAL250005054088 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/203 `/scratch/stefan/7922901/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005054088.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054088 none COC(C(=O)NCCN(C)C(=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.3', '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, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 163, 128, 128, 128, 82, 54, 23, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 163, 201, 201, 173, 173, 173, 163, 128, 82, 82, 54, 54, 23, 23, 23, 1, 201, 201, 201, 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, 38, 39, 40]) total number of confs: 903 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054088 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054088 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054088/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054088 Building REAL250005054089 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054089' /scratch/stefan/7922901/working/building/REAL250005054089 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054089 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054089/0 /scratch/stefan/7922901/working/building/REAL250005054089 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/204 `/scratch/stefan/7922901/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054089.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054089 none CC1CC1CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 72, 72, 72, 63, 42, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 175, 175, 72, 63, 63, 42, 42, 18, 18, 18, 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: 841 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054089 none CC1CC1CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 33, 33, 33, 71, 87, 122, 122, 187, 187, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 5, 5, 33, 71, 71, 87, 87, 122, 122, 122, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/7922901/working/building/REAL250005054089 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054089 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054089/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054089 Building REAL250005054090 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054090' /scratch/stefan/7922901/working/building/REAL250005054090 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054090 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054090/0 /scratch/stefan/7922901/working/building/REAL250005054090 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/205 `/scratch/stefan/7922901/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(CC)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054090.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054090 none C=CC(C)(CC)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 172, 110, 172, 172, 198, 110, 110, 57, 47, 20, 9, 20, 1, 9, 1, 1, 1, 1, 1, 1, 198, 198, 198, 172, 172, 172, 201, 201, 201, 201, 201, 110, 57, 57, 47, 47, 20, 20, 20, 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: 981 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054090 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054090 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054090/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054090 Building REAL250005054091 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054091' /scratch/stefan/7922901/working/building/REAL250005054091 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054091 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054091/0 /scratch/stefan/7922901/working/building/REAL250005054091 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/206 `/scratch/stefan/7922901/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C[C@H]1CCOC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054091.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054091 none CN(CCNC(=O)C[C@H]1CCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 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: [17, 6, 17, 32, 35, 65, 65, 65, 158, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 32, 32, 35, 35, 65, 158, 158, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 792 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054091 none CN(CCNC(=O)C[C@H]1CCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 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: [174, 142, 99, 34, 34, 10, 34, 1, 1, 1, 1, 1, 1, 1, 174, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 142, 142, 99, 99, 34, 10, 10, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 827 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054091 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054091 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054091/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054091 Building REAL250005054092 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054092' /scratch/stefan/7922901/working/building/REAL250005054092 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054092 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054092/0 /scratch/stefan/7922901/working/building/REAL250005054092 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/207 `/scratch/stefan/7922901/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054092.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054092 none CCC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 180, 75, 75, 75, 53, 46, 18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 1, 180, 180, 201, 201, 201, 201, 201, 75, 53, 53, 46, 46, 18, 18, 18, 1, 180, 180, 180, 180] 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: 705 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: REAL250005054092 none CCC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 7, 7, 7, 35, 57, 92, 92, 162, 162, 180, 180, 180, 180, 180, 1, 1, 3, 3, 3, 3, 3, 7, 35, 35, 57, 57, 92, 92, 92, 180, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 36, 37, 35, 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, 32, 33]) total number of confs: 646 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054092 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054092 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054092/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054092 Building REAL250005054093 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054093' /scratch/stefan/7922901/working/building/REAL250005054093 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054093 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054093/0 /scratch/stefan/7922901/working/building/REAL250005054093 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/208 `/scratch/stefan/7922901/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC(C)(F)F)C(=O)C1=CC(=O)[N-]O1) `REAL250005054093.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054093 none CN(CCNC(=O)CC(C)(F)F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 34, 38, 65, 65, 65, 159, 191, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 34, 34, 38, 38, 65, 159, 159, 201, 201, 201, 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: 925 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054093 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054093 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054093/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054093 Building REAL250005054094 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054094' /scratch/stefan/7922901/working/building/REAL250005054094 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054094 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054094/0 /scratch/stefan/7922901/working/building/REAL250005054094 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/209 `/scratch/stefan/7922901/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054094.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054094 none CCCC1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 187, 75, 75, 75, 52, 41, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 187, 187, 201, 201, 201, 201, 201, 198, 198, 75, 52, 52, 41, 41, 16, 16, 16, 1, 187, 187, 187, 187] 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: 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: REAL250005054094 none CCCC1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 1, 1, 1, 6, 6, 6, 40, 74, 108, 108, 171, 171, 187, 187, 187, 187, 187, 1, 1, 5, 5, 5, 5, 5, 4, 4, 6, 40, 40, 74, 74, 108, 108, 108, 187, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 37, 38, 39, 40, 19, 20] 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, 35, 36]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054094 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054094 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054094/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054094 Building REAL250005054095 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054095' /scratch/stefan/7922901/working/building/REAL250005054095 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054095 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054095/0 /scratch/stefan/7922901/working/building/REAL250005054095 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/210 `/scratch/stefan/7922901/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1C[C@H]1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054095.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054095 none CCC[C@@H]1C[C@H]1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 114, 114, 114, 114, 34, 114, 34, 34, 27, 23, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 114, 114, 34, 27, 27, 23, 23, 13, 13, 13, 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: 852 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054095 none CCC[C@@H]1C[C@H]1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 36, 57, 74, 74, 101, 101, 114, 114, 114, 114, 114, 12, 12, 12, 12, 12, 6, 6, 1, 1, 11, 36, 36, 57, 57, 74, 74, 74, 114] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 499 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054095 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054095 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054095/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054095 Building REAL250005054096 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054096' /scratch/stefan/7922901/working/building/REAL250005054096 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054096 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054096/0 /scratch/stefan/7922901/working/building/REAL250005054096 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/211 `/scratch/stefan/7922901/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054096.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054096 none CC(C)C1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 120, 120, 120, 70, 54, 23, 10, 23, 1, 10, 1, 1, 1, 1, 1, 1, 200, 200, 201, 201, 201, 201, 201, 201, 201, 120, 70, 70, 54, 54, 23, 23, 23, 1, 200, 200, 200, 200] 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: 693 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: REAL250005054096 none CC(C)C1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 6, 6, 6, 32, 61, 91, 91, 163, 163, 200, 200, 200, 200, 200, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 32, 32, 61, 61, 91, 91, 91, 200, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 37, 38, 39, 40, 19, 20] set([0, 2, 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, 35, 36]) total number of confs: 697 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054096 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054096 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054096/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054096 Building REAL250005054097 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054097' /scratch/stefan/7922901/working/building/REAL250005054097 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054097 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054097/0 /scratch/stefan/7922901/working/building/REAL250005054097 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/212 `/scratch/stefan/7922901/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C)(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054097.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054097 none C=C1CC(C)(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 102, 201, 102, 102, 69, 59, 21, 10, 21, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 102, 69, 69, 59, 59, 21, 21, 21, 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: 674 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: REAL250005054097 none C=C1CC(C)(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 54, 93, 93, 184, 184, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 6, 30, 30, 54, 54, 93, 93, 93, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 23, 24, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 698 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054097 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054097 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054097/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054097 Building REAL250005054098 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054098' /scratch/stefan/7922901/working/building/REAL250005054098 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054098 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054098/0 /scratch/stefan/7922901/working/building/REAL250005054098 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/213 `/scratch/stefan/7922901/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(CF)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054098.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054098 none CN(CCNC(=O)C1(CF)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 20, 41, 46, 91, 91, 91, 188, 201, 188, 188, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 41, 41, 46, 46, 91, 201, 201, 188, 188, 188, 188, 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: 689 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: REAL250005054098 none CN(CCNC(=O)C1(CF)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 64, 38, 7, 7, 1, 7, 1, 1, 10, 1, 1, 107, 176, 176, 188, 188, 188, 188, 188, 107, 107, 107, 64, 64, 38, 38, 7, 10, 10, 1, 1, 1, 1, 188] 201 rigid atoms, others: [32, 33, 5, 7, 8, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 6, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 700 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054098 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054098 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054098/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054098 Building REAL250005054099 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054099' /scratch/stefan/7922901/working/building/REAL250005054099 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054099 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054099/0 /scratch/stefan/7922901/working/building/REAL250005054099 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/214 `/scratch/stefan/7922901/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC2(CC2)C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054099.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054099 none CN(CCNC(=O)C1CC2(CC2)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 43, 57, 83, 83, 83, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 43, 43, 57, 57, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005054099 none CN(CCNC(=O)C1CC2(CC2)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 82, 45, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 119, 191, 191, 201, 201, 201, 201, 201, 119, 119, 119, 82, 82, 45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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/7922901/working/building/REAL250005054099 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054099 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054099/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054099 Building REAL250005054100 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054100' /scratch/stefan/7922901/working/building/REAL250005054100 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054100 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054100/0 /scratch/stefan/7922901/working/building/REAL250005054100 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/215 `/scratch/stefan/7922901/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(C)(C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054100.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054100 none CN(CCNC(=O)C(C)(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [23, 10, 23, 54, 74, 103, 103, 103, 115, 115, 115, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 54, 54, 74, 74, 103, 115, 115, 115, 115, 115, 115, 115, 115, 115, 1] 115 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: 478 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054100 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054100 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054100/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054100 Building REAL250005054101 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054101' /scratch/stefan/7922901/working/building/REAL250005054101 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054101 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054101/0 /scratch/stefan/7922901/working/building/REAL250005054101 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/216 `/scratch/stefan/7922901/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054101.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054101 none CCCCCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 177, 56, 56, 56, 48, 37, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 56, 48, 48, 37, 37, 18, 18, 18, 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: 870 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054101 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054101 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054101/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054101 Building REAL250005054102 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054102' /scratch/stefan/7922901/working/building/REAL250005054102 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054102 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054102/0 /scratch/stefan/7922901/working/building/REAL250005054102 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/217 `/scratch/stefan/7922901/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054102.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054102 none CC[N@H+](C)CCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 15, 15, 9, 9, 9, 9, 9, 9, 9, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 15 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: 61 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054102 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054102/1 /scratch/stefan/7922901/working/building/REAL250005054102 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/218 `/scratch/stefan/7922901/working/3D/218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054102.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005054102 none CC[N@@H+](C)CCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 15, 15, 9, 9, 9, 9, 9, 9, 9, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 15 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: 61 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054102 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054102 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054102/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054102/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054102 Building REAL250005054103 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054103' /scratch/stefan/7922901/working/building/REAL250005054103 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054103 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054103/0 /scratch/stefan/7922901/working/building/REAL250005054103 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/219 `/scratch/stefan/7922901/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CON=C1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054103.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054103 none CC1=CON=C1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 193, 193, 193, 81, 51, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 193, 81, 81, 51, 51, 21, 21, 21, 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: 689 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: REAL250005054103 none CC1=CON=C1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 4, 4, 4, 24, 48, 95, 95, 178, 178, 201, 201, 201, 201, 201, 2, 2, 2, 1, 4, 24, 24, 48, 48, 95, 95, 95, 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: 679 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054103 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054103 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054103/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054103 Building REAL250005054104 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054104' /scratch/stefan/7922901/working/building/REAL250005054104 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054104 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054104/0 /scratch/stefan/7922901/working/building/REAL250005054104 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/220 `/scratch/stefan/7922901/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1C[C@H]1C(N)=O)C(=O)C1=CC(=O)[N-]O1) `REAL250005054104.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054104 none CN(CCNC(=O)[C@H]1C[C@H]1C(N)=O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 19, 19, 33, 33, 33, 53, 53, 53, 53, 53, 55, 55, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 19, 19, 19, 19, 33, 53, 53, 55, 55, 1] 55 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054104 none CN(CCNC(=O)[C@H]1C[C@H]1C(N)=O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 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 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [42, 31, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 6, 6, 42, 49, 49, 53, 53, 53, 53, 53, 42, 42, 42, 31, 31, 24, 24, 7, 1, 1, 6, 6, 53] 55 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054104 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054104 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054104/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054104 Building REAL250005054105 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054105' /scratch/stefan/7922901/working/building/REAL250005054105 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054105 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054105/0 /scratch/stefan/7922901/working/building/REAL250005054105 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/221 `/scratch/stefan/7922901/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005054105.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054105 none CC[C@@H](C(=O)NCCN(C)C(=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.3', '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, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 9, 9, 6, 4, 6, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 9, 9, 6, 6, 6, 1, 10, 10, 10, 10, 10, 10] 10 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: 39 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054105 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054105 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054105/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054105 Building REAL250005054106 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054106' /scratch/stefan/7922901/working/building/REAL250005054106 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054106 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054106/0 /scratch/stefan/7922901/working/building/REAL250005054106 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/222 `/scratch/stefan/7922901/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(CF)CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054106.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054106 none CN(CCNC(=O)C1(CF)CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 6, 23, 45, 47, 95, 95, 95, 198, 201, 198, 198, 198, 1, 6, 1, 1, 1, 1, 1, 1, 23, 23, 23, 45, 45, 47, 47, 95, 201, 201, 198, 198, 198, 198, 198, 198, 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: 637 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054106 none CN(CCNC(=O)C1(CF)CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 62, 35, 6, 6, 1, 6, 1, 1, 10, 1, 1, 1, 112, 182, 182, 198, 198, 198, 198, 198, 112, 112, 112, 62, 62, 35, 35, 6, 10, 10, 1, 1, 1, 1, 1, 1, 198] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 736 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054106 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054106 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054106/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054106 Building REAL250005054107 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054107' /scratch/stefan/7922901/working/building/REAL250005054107 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054107 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054107/0 /scratch/stefan/7922901/working/building/REAL250005054107 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/223 `/scratch/stefan/7922901/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CN1C=NC=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054107.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054107 none CN(CCNC(=O)CN1C=NC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 27, 27, 56, 56, 56, 160, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 56, 160, 160, 201, 201, 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: REAL250005054107 none CN(CCNC(=O)CN1C=NC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 153, 121, 42, 42, 8, 42, 1, 1, 1, 1, 1, 1, 172, 198, 198, 201, 201, 201, 201, 201, 172, 172, 172, 153, 153, 121, 121, 42, 8, 8, 1, 1, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 806 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054107 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054107 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054107/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054107 Building REAL250005054108 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054108' /scratch/stefan/7922901/working/building/REAL250005054108 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054108 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054108/0 /scratch/stefan/7922901/working/building/REAL250005054108 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/224 `/scratch/stefan/7922901/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1=NNC=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054108.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054108 none CN(CCNC(=O)CC1=NNC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 21, 21, 36, 36, 36, 71, 113, 113, 113, 113, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 21, 21, 21, 21, 36, 71, 71, 113, 113, 1] 113 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: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054108 none CN(CCNC(=O)CC1=NNC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [106, 101, 96, 43, 43, 8, 43, 1, 1, 1, 1, 1, 1, 106, 113, 113, 113, 113, 113, 113, 113, 106, 106, 106, 101, 101, 96, 96, 43, 8, 8, 1, 1, 113] 113 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054108 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054108/1 /scratch/stefan/7922901/working/building/REAL250005054108 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/225 `/scratch/stefan/7922901/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1=NN=CN1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054108.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054108 none CN(CCNC(=O)CC1=NN=CN1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 5, 1, 8, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 13, 15, 15, 23, 23, 23, 37, 39, 39, 39, 39, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 15, 15, 15, 15, 23, 37, 37, 39, 39, 1] 39 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: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054108 none CN(CCNC(=O)CC1=NN=CN1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 5, 1, 8, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 31, 13, 13, 6, 13, 1, 1, 1, 1, 1, 1, 37, 39, 39, 39, 39, 39, 39, 39, 37, 37, 37, 37, 37, 31, 31, 13, 6, 6, 1, 1, 39] 39 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054108 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054108 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054108/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054108/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054108 Building REAL250005054109 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054109' /scratch/stefan/7922901/working/building/REAL250005054109 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054109 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054109/0 /scratch/stefan/7922901/working/building/REAL250005054109 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/226 `/scratch/stefan/7922901/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054109.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054109 none CC(C)C(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 200, 107, 193, 107, 107, 68, 50, 19, 9, 19, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 193, 107, 68, 68, 50, 50, 19, 19, 19, 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: 848 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054109 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054109 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054109/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054109 Building REAL250005054110 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054110' /scratch/stefan/7922901/working/building/REAL250005054110 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054110 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054110/0 /scratch/stefan/7922901/working/building/REAL250005054110 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/227 `/scratch/stefan/7922901/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054110.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054110 none CC[C@@H]1C[C@H]1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 159, 159, 159, 159, 58, 159, 58, 58, 36, 30, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 159, 159, 58, 36, 36, 30, 30, 15, 15, 15, 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: 743 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054110 none CC[C@@H]1C[C@H]1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 41, 62, 95, 95, 147, 147, 159, 159, 159, 159, 159, 3, 3, 3, 3, 3, 1, 1, 12, 41, 41, 62, 62, 95, 95, 95, 159] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054110 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054110 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054110/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054110 Building REAL250005054111 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054111' /scratch/stefan/7922901/working/building/REAL250005054111 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054111 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054111/0 /scratch/stefan/7922901/working/building/REAL250005054111 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/228 `/scratch/stefan/7922901/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054111.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054111 none CC(C)CCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 170, 177, 48, 48, 48, 40, 35, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 48, 40, 40, 35, 35, 16, 16, 16, 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: 1238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054111 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054111 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054111/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054111 Building REAL250005054112 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054112' /scratch/stefan/7922901/working/building/REAL250005054112 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054112 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054112/0 /scratch/stefan/7922901/working/building/REAL250005054112 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/229 `/scratch/stefan/7922901/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC12CC2)C(=O)C1=CC(=O)[N-]O1) `REAL250005054112.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054112 none CN(CCNC(=O)C1CC12CC2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 20, 48, 59, 90, 90, 90, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 48, 48, 59, 59, 90, 201, 201, 201, 201, 201, 201, 201, 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: 662 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: REAL250005054112 none CN(CCNC(=O)C1CC12CC2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 96, 63, 13, 13, 1, 13, 1, 1, 1, 1, 1, 128, 192, 192, 201, 201, 201, 201, 201, 128, 128, 128, 96, 96, 63, 63, 13, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35]) total number of confs: 768 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054112 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054112 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054112/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054112 Building REAL250005054113 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054113' /scratch/stefan/7922901/working/building/REAL250005054113 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054113 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054113/0 /scratch/stefan/7922901/working/building/REAL250005054113 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/230 `/scratch/stefan/7922901/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1=CNC=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054113.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054113 none CN(CCNC(=O)CC1=CNC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 18, 31, 31, 58, 58, 58, 152, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 31, 31, 31, 31, 58, 152, 152, 201, 201, 201, 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: 663 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054113 none CN(CCNC(=O)CC1=CNC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 148, 111, 33, 33, 9, 33, 1, 1, 1, 1, 1, 1, 172, 201, 201, 201, 201, 201, 201, 201, 172, 172, 172, 148, 148, 111, 111, 33, 9, 9, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 820 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054113 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054113/1 /scratch/stefan/7922901/working/building/REAL250005054113 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/231 `/scratch/stefan/7922901/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1=CN=CN1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054113.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054113 none CN(CCNC(=O)CC1=CN=CN1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 8, 12, 18, 18, 23, 23, 23, 48, 58, 58, 58, 58, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 18, 18, 18, 18, 23, 48, 48, 58, 58, 58, 1] 58 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: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054113 none CN(CCNC(=O)CC1=CN=CN1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [56, 54, 43, 18, 18, 4, 18, 1, 1, 1, 1, 1, 1, 56, 58, 58, 58, 58, 58, 58, 58, 56, 56, 56, 54, 54, 43, 43, 18, 4, 4, 1, 1, 1, 58] 58 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054113 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054113 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054113/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054113/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054113 Building REAL250005054114 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054114' /scratch/stefan/7922901/working/building/REAL250005054114 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054114 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054114/0 /scratch/stefan/7922901/working/building/REAL250005054114 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/232 `/scratch/stefan/7922901/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1CC(=O)N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054114.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054114 none CN(CCNC(=O)[C@@H]1CC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [22, 9, 22, 32, 32, 55, 55, 55, 94, 94, 94, 94, 94, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 22, 32, 32, 32, 32, 55, 94, 94, 94, 1] 94 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: 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: REAL250005054114 none CN(CCNC(=O)[C@@H]1CC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [75, 65, 42, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 75, 94, 94, 94, 94, 94, 94, 94, 75, 75, 75, 65, 65, 42, 42, 10, 1, 1, 1, 94] 94 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054114 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054114 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054114/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054114 Building REAL250005054115 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054115' /scratch/stefan/7922901/working/building/REAL250005054115 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054115 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054115/0 /scratch/stefan/7922901/working/building/REAL250005054115 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/233 `/scratch/stefan/7922901/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CCCCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054115.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054115 none CN(CCNC(=O)C1=CCCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 25, 61, 78, 127, 127, 127, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 61, 61, 78, 78, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005054115 none CN(CCNC(=O)C1=CCCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 83, 51, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 126, 189, 189, 201, 201, 201, 201, 201, 126, 126, 126, 83, 83, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38]) total number of confs: 757 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054115 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054115 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054115/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054115 Building REAL250005054116 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054116' /scratch/stefan/7922901/working/building/REAL250005054116 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054116 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054116/0 /scratch/stefan/7922901/working/building/REAL250005054116 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/234 `/scratch/stefan/7922901/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005054116.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054116 none CC(=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C(C)C 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.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 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: [199, 199, 107, 107, 107, 66, 48, 17, 8, 17, 1, 8, 1, 1, 1, 1, 1, 1, 199, 201, 201, 199, 199, 199, 199, 107, 66, 66, 48, 48, 17, 17, 17, 1, 201, 201, 201, 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, 38, 39, 40]) total number of confs: 712 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054116 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054116 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054116/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054116 Building REAL250005054117 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054117' /scratch/stefan/7922901/working/building/REAL250005054117 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054117 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054117/0 /scratch/stefan/7922901/working/building/REAL250005054117 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/235 `/scratch/stefan/7922901/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1CC(=O)N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054117.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054117 none CN(CCNC(=O)[C@H]1CC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [21, 9, 21, 31, 31, 51, 51, 51, 91, 91, 91, 91, 91, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 31, 31, 31, 31, 51, 91, 91, 91, 1] 91 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: 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: REAL250005054117 none CN(CCNC(=O)[C@H]1CC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 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 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [73, 65, 43, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 73, 91, 91, 91, 91, 91, 91, 91, 73, 73, 73, 65, 65, 43, 43, 10, 1, 1, 1, 91] 91 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054117 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054117 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054117/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054117 Building REAL250005054118 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054118' /scratch/stefan/7922901/working/building/REAL250005054118 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054118 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054118/0 /scratch/stefan/7922901/working/building/REAL250005054118 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/236 `/scratch/stefan/7922901/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CN1C=NC=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054118.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054118 none CN(CCNC(=O)CN1C=NC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 27, 27, 56, 56, 56, 160, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 56, 160, 160, 201, 201, 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: REAL250005054118 none CN(CCNC(=O)CN1C=NC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 153, 121, 42, 42, 8, 42, 1, 1, 1, 1, 1, 1, 172, 198, 198, 201, 201, 201, 201, 201, 172, 172, 172, 153, 153, 121, 121, 42, 8, 8, 1, 1, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 806 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054118 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054118 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054118/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054118 Building REAL250005054119 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054119' /scratch/stefan/7922901/working/building/REAL250005054119 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054119 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054119/0 /scratch/stefan/7922901/working/building/REAL250005054119 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/237 `/scratch/stefan/7922901/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054119.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054119 none COC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 129, 129, 77, 55, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 129, 77, 77, 55, 55, 22, 22, 22, 1, 201, 201, 201, 201] 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: 722 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054119 none COC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 10, 49, 79, 110, 110, 164, 164, 201, 201, 201, 201, 201, 1, 1, 4, 4, 4, 10, 49, 49, 79, 79, 110, 110, 110, 201, 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: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054119 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054119 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054119/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054119 Building REAL250005054120 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054120' /scratch/stefan/7922901/working/building/REAL250005054120 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054120 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054120/0 /scratch/stefan/7922901/working/building/REAL250005054120 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/238 `/scratch/stefan/7922901/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CSC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054120.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054120 none CN(CCNC(=O)C1CSC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 14, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 8, 26, 54, 66, 105, 105, 105, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 26, 54, 54, 66, 66, 105, 201, 201, 201, 201, 201, 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: 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: REAL250005054120 none CN(CCNC(=O)C1CSC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 14, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 87, 53, 9, 9, 1, 9, 1, 1, 1, 1, 123, 195, 195, 201, 201, 201, 201, 201, 123, 123, 123, 87, 87, 53, 53, 9, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32]) total number of confs: 779 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054120 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054120 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054120/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054120 Building REAL250005054121 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054121' /scratch/stefan/7922901/working/building/REAL250005054121 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054121 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054121/0 /scratch/stefan/7922901/working/building/REAL250005054121 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/239 `/scratch/stefan/7922901/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(O)CCCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054121.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054121 none CN(CCNC(=O)C1(O)CCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 234 conformations in input total number of sets (complete confs): 234 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 23, 23, 46, 46, 46, 78, 78, 78, 78, 78, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 23, 23, 23, 23, 46, 234, 78, 78, 78, 78, 78, 78, 78, 78, 1] 234 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: 489 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: REAL250005054121 none CN(CCNC(=O)C1(O)CCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 234 conformations in input total number of sets (complete confs): 234 using faster count positions algorithm for large data unique positions, atoms: [64, 54, 42, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 64, 78, 78, 78, 78, 78, 78, 78, 64, 64, 64, 54, 54, 42, 42, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 78] 234 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38]) total number of confs: 306 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054121 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054121 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054121/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054121 Building REAL250005054122 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054122' /scratch/stefan/7922901/working/building/REAL250005054122 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054122 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054122/0 /scratch/stefan/7922901/working/building/REAL250005054122 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/240 `/scratch/stefan/7922901/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054122.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054122 none C=CCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 97, 97, 97, 75, 56, 23, 10, 23, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 97, 75, 75, 56, 56, 23, 23, 23, 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: 848 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054122 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054122 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054122/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054122 Building REAL250005054123 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054123' /scratch/stefan/7922901/working/building/REAL250005054123 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054123 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054123/0 /scratch/stefan/7922901/working/building/REAL250005054123 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/241 `/scratch/stefan/7922901/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C[NH+](C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054123.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054123 none CN(CCNC(=O)C[NH+](C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 1, 10, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 17 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: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054123 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054123/1 /scratch/stefan/7922901/working/building/REAL250005054123 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/242 `/scratch/stefan/7922901/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054123.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005054123 none CN(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 141, 141, 141, 79, 53, 23, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 141, 79, 79, 53, 53, 23, 23, 23, 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: 870 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054123 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054123 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054123/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054123/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054123 Building REAL250005054124 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054124' /scratch/stefan/7922901/working/building/REAL250005054124 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054124 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054124/0 /scratch/stefan/7922901/working/building/REAL250005054124 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/243 `/scratch/stefan/7922901/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054124.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054124 none C=CC(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 136, 201, 136, 136, 76, 60, 26, 9, 26, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 136, 76, 76, 60, 60, 26, 26, 26, 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: 1382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054124 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054124 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054124/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054124 Building REAL250005054125 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054125' /scratch/stefan/7922901/working/building/REAL250005054125 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054125 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054125/0 /scratch/stefan/7922901/working/building/REAL250005054125 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/244 `/scratch/stefan/7922901/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCCN=[N+]=[N-])C(=O)C1=CC(=O)[N-]O1) `REAL250005054125.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054125 none CN(CCNC(=O)CCCN=[N+]=[N-])C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 9, 15, 15, 21, 21, 21, 70, 77, 149, 201, 201, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 21, 70, 70, 102, 102, 134, 133, 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: 862 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054125 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054125 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054125/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054125 Building REAL250005054126 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054126' /scratch/stefan/7922901/working/building/REAL250005054126 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054126 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054126/0 /scratch/stefan/7922901/working/building/REAL250005054126 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/245 `/scratch/stefan/7922901/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1OCC1(C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054126.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054126 none CN(CCNC(=O)C1OCC1(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 18, 29, 29, 53, 53, 53, 70, 70, 70, 70, 70, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 29, 29, 29, 29, 53, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1] 70 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: 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: REAL250005054126 none CN(CCNC(=O)C1OCC1(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [54, 45, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 54, 69, 69, 70, 70, 70, 70, 70, 54, 54, 54, 45, 45, 28, 28, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 70] 70 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054126 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054126 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054126/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054126 Building REAL250005054127 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054127' /scratch/stefan/7922901/working/building/REAL250005054127 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054127 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054127/0 /scratch/stefan/7922901/working/building/REAL250005054127 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/246 `/scratch/stefan/7922901/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)N1CCC1) `REAL250005054127.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054127 none CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 10, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 11, 11, 11, 44, 69, 104, 104, 132, 132, 142, 142, 142, 142, 142, 1, 1, 1, 1, 4, 4, 4, 4, 11, 44, 44, 69, 69, 104, 104, 104, 142, 1, 1, 1, 1, 1, 1] 142 rigid atoms, others: [1, 34, 35, 36, 37, 38, 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, 33]) total number of confs: 527 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: REAL250005054127 none CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 10, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 134, 134, 134, 77, 56, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 142, 142, 142, 142, 134, 77, 77, 56, 56, 17, 17, 17, 1, 142, 142, 142, 142, 142, 142] 142 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: 555 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054127 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054127/1 /scratch/stefan/7922901/working/building/REAL250005054127 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/247 `/scratch/stefan/7922901/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)[NH+]1CCC1) `REAL250005054127.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054127 none CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)[NH+]1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'H', '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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 6, 6, 6, 6, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [1, 35, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054127 none CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)[NH+]1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'H', '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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 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 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, 8, 8, 7, 5, 7, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 7, 7, 7, 1, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [34, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054127 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054127 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054127/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054127/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054127 Building REAL250005054128 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054128' /scratch/stefan/7922901/working/building/REAL250005054128 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054128 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054128/0 /scratch/stefan/7922901/working/building/REAL250005054128 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/248 `/scratch/stefan/7922901/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1CC1(F)F)C(=O)C1=CC(=O)[N-]O1) `REAL250005054128.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054128 none CN(CCNC(=O)[C@H]1CC1(F)F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 8, 23, 46, 55, 95, 95, 95, 173, 173, 173, 173, 173, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 46, 46, 55, 55, 95, 173, 173, 1] 173 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: 585 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054128 none CN(CCNC(=O)[C@H]1CC1(F)F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [133, 91, 59, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 133, 172, 172, 173, 173, 173, 173, 173, 133, 133, 133, 91, 91, 59, 59, 13, 1, 1, 173] 173 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 682 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054128 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054128 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054128/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054128 Building REAL250005054129 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054129' /scratch/stefan/7922901/working/building/REAL250005054129 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054129 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054129/0 /scratch/stefan/7922901/working/building/REAL250005054129 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/249 `/scratch/stefan/7922901/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1=CNN=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054129.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054129 none CN(CCNC(=O)CC1=CNN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 8, 22, 38, 38, 86, 86, 86, 166, 172, 172, 172, 172, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 38, 38, 38, 38, 86, 166, 166, 172, 172, 172, 1] 172 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: 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: REAL250005054129 none CN(CCNC(=O)CC1=CNN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 106, 69, 21, 21, 7, 21, 1, 1, 1, 1, 1, 1, 144, 197, 197, 201, 201, 201, 201, 201, 144, 144, 144, 106, 106, 69, 69, 21, 7, 7, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 804 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054129 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054129 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054129/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054129 Building REAL250005054130 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054130' /scratch/stefan/7922901/working/building/REAL250005054130 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054130 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054130/0 /scratch/stefan/7922901/working/building/REAL250005054130 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/250 `/scratch/stefan/7922901/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054130.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054130 none CC(C)NC(=O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 201, 199, 144, 199, 144, 144, 77, 47, 23, 12, 23, 1, 12, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 199, 144, 77, 77, 47, 47, 23, 23, 23, 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: 719 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054130 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054130 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054130/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054130 Building REAL250005054131 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054131' /scratch/stefan/7922901/working/building/REAL250005054131 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054131 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054131/0 /scratch/stefan/7922901/working/building/REAL250005054131 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/251 `/scratch/stefan/7922901/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005054131.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054131 none CC1=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCO1 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.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 122, 122, 67, 51, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 122, 67, 67, 51, 51, 16, 16, 16, 1, 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]) total number of confs: 569 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054131 none CC1=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCO1 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.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 73, 113, 113, 193, 193, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 9, 45, 45, 73, 73, 113, 113, 113, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 36, 35, 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: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054131 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054131 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054131/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054131 Building REAL250005054132 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054132' /scratch/stefan/7922901/working/building/REAL250005054132 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054132 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054132/0 /scratch/stefan/7922901/working/building/REAL250005054132 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/252 `/scratch/stefan/7922901/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C=C1CCCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054132.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054132 none CN(CCNC(=O)C=C1CCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 51, 60, 99, 99, 99, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 21, 21, 21, 51, 51, 60, 60, 99, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005054132 none CN(CCNC(=O)C=C1CCCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 85, 47, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 130, 191, 191, 201, 201, 201, 201, 201, 130, 130, 130, 85, 85, 47, 47, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38]) total number of confs: 777 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054132 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054132 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054132/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054132 Building REAL250005054133 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054133' /scratch/stefan/7922901/working/building/REAL250005054133 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005054133 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054133/0 /scratch/stefan/7922901/working/building/REAL250005054133 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/253 `/scratch/stefan/7922901/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C[N@H+](C)C1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054133.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054133 none CN(CCNC(=O)C[N@H+](C)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 12, 12, 12, 13, 13, 13, 13, 13, 13, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1] 13 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: 39 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054133 none CN(CCNC(=O)C[N@H+](C)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 11, 8, 8, 4, 8, 2, 1, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 11, 11, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 13] 13 rigid atoms, others: [35, 36, 37, 38, 39, 8, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40]) total number of confs: 56 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054133 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054133/1 /scratch/stefan/7922901/working/building/REAL250005054133 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/254 `/scratch/stefan/7922901/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C[N@@H+](C)C1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054133.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054133 none CN(CCNC(=O)C[N@@H+](C)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 11, 11, 11, 12, 12, 12, 12, 12, 12, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 12 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: 37 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: REAL250005054133 none CN(CCNC(=O)C[N@@H+](C)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 11, 9, 9, 6, 9, 2, 1, 2, 2, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 9, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 12] 12 rigid atoms, others: [35, 36, 37, 38, 39, 8, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40]) total number of confs: 51 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054133 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `2' /scratch/stefan/7922901/working/building/REAL250005054133/2 /scratch/stefan/7922901/working/building/REAL250005054133 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 2 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/255 `/scratch/stefan/7922901/working/3D/255' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CN(C)C1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054133.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005054133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054133/2/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: REAL250005054133 none CN(CCNC(=O)CN(C)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 27, 27, 65, 65, 65, 158, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 27, 27, 27, 27, 65, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 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: 772 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054133 none CN(CCNC(=O)CN(C)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 145, 113, 37, 37, 11, 37, 3, 1, 3, 1, 1, 1, 171, 200, 200, 201, 201, 201, 201, 201, 171, 171, 171, 145, 145, 113, 113, 37, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 813 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054133 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054133 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054133/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054133/1.* 2: /scratch/stefan/7922901/working/building/REAL250005054133/2.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054133 Building REAL250005054134 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054134' /scratch/stefan/7922901/working/building/REAL250005054134 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054134 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054134/0 /scratch/stefan/7922901/working/building/REAL250005054134 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/256 `/scratch/stefan/7922901/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(CO)COC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054134.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054134 none CN(CCNC(=O)C1(CO)COC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 3, 7, 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: [25, 9, 25, 46, 49, 100, 100, 100, 187, 201, 187, 187, 187, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 46, 46, 49, 49, 100, 201, 201, 603, 187, 187, 187, 187, 1] 603 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: 1296 number of broken/clashed sets: 299 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054134 none CN(CCNC(=O)C1(CO)COC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 3, 7, 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: [112, 66, 39, 7, 7, 1, 7, 1, 1, 10, 1, 1, 1, 112, 168, 168, 187, 187, 187, 187, 187, 112, 112, 112, 66, 66, 39, 39, 7, 10, 10, 30, 1, 1, 1, 1, 187] 603 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 727 number of broken/clashed sets: 299 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054134 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054134 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054134/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054134 Building REAL250005054135 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054135' /scratch/stefan/7922901/working/building/REAL250005054135 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054135 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054135/0 /scratch/stefan/7922901/working/building/REAL250005054135 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/257 `/scratch/stefan/7922901/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054135.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054135 none CC(C)=CCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 193, 67, 67, 67, 63, 45, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 67, 63, 63, 45, 45, 17, 17, 17, 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: 870 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054135 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054135 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054135/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054135 Building REAL250005054136 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054136' /scratch/stefan/7922901/working/building/REAL250005054136 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054136 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054136/0 /scratch/stefan/7922901/working/building/REAL250005054136 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/258 `/scratch/stefan/7922901/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1COC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054136.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054136 none CN(CCNC(=O)C1COC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 8, 27, 54, 64, 106, 106, 106, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 27, 27, 27, 54, 54, 64, 64, 106, 201, 201, 201, 201, 201, 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: 691 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054136 none CN(CCNC(=O)C1COC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 85, 47, 9, 9, 1, 9, 1, 1, 1, 1, 129, 193, 193, 201, 201, 201, 201, 201, 129, 129, 129, 85, 85, 47, 47, 9, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32]) total number of confs: 779 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054136 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054136 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054136/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054136 Building REAL250005054137 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054137' /scratch/stefan/7922901/working/building/REAL250005054137 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054137 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054137/0 /scratch/stefan/7922901/working/building/REAL250005054137 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/259 `/scratch/stefan/7922901/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)O1) `REAL250005054137.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054137 none CC1CCC(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 201, 201, 201, 152, 152, 152, 86, 56, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 86, 86, 56, 56, 20, 20, 20, 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: 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: REAL250005054137 none CC1CCC(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 10, 10, 10, 48, 79, 124, 124, 190, 190, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 48, 48, 79, 79, 124, 124, 124, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 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: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054137 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054137 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054137/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054137 Building REAL250005054138 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054138' /scratch/stefan/7922901/working/building/REAL250005054138 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054138 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054138/0 /scratch/stefan/7922901/working/building/REAL250005054138 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/260 `/scratch/stefan/7922901/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1(CO)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054138.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054138 none CN(CCNC(=O)CC1(CO)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 7, 16, 30, 32, 62, 62, 62, 151, 196, 201, 196, 196, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 30, 30, 32, 32, 62, 151, 151, 201, 201, 603, 196, 196, 196, 196, 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: 1391 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: REAL250005054138 none CN(CCNC(=O)CC1(CO)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [161, 134, 97, 28, 28, 6, 28, 1, 1, 1, 10, 1, 1, 161, 186, 186, 196, 196, 196, 196, 196, 161, 161, 161, 134, 134, 97, 97, 28, 6, 6, 10, 10, 30, 1, 1, 1, 1, 196] 603 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 829 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054138 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054138 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054138/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054138 Building REAL250005054139 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054139' /scratch/stefan/7922901/working/building/REAL250005054139 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054139 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054139/0 /scratch/stefan/7922901/working/building/REAL250005054139 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/261 `/scratch/stefan/7922901/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1C[NH+](C)C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054139.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054139 none CN(CCNC(=O)CC1C[NH+](C)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 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: [20, 11, 20, 27, 27, 29, 29, 29, 45, 45, 45, 45, 45, 45, 1, 11, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 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: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054139 none CN(CCNC(=O)CC1C[NH+](C)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 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: [40, 34, 34, 19, 19, 6, 19, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 45, 45, 45, 45, 45, 40, 40, 40, 34, 34, 34, 34, 19, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1, 45] 45 rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 40]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054139 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054139 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054139/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054139 Building REAL250005054140 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054140' /scratch/stefan/7922901/working/building/REAL250005054140 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054140 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054140/0 /scratch/stefan/7922901/working/building/REAL250005054140 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/262 `/scratch/stefan/7922901/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC(C)(O)C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054140.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054140 none CN(CCNC(=O)C1CC(C)(O)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 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: [25, 7, 25, 51, 63, 108, 108, 108, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 25, 25, 25, 51, 51, 63, 63, 108, 201, 201, 201, 201, 201, 201, 603, 201, 201, 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: 1286 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054140 none CN(CCNC(=O)C1CC(C)(O)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 6, 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: [124, 87, 51, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 124, 191, 191, 201, 201, 201, 201, 201, 124, 124, 124, 87, 87, 51, 51, 12, 1, 1, 1, 2, 2, 2, 6, 1, 1, 201] 603 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 38]) total number of confs: 764 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054140 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054140 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054140/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054140 Building REAL250005054141 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054141' /scratch/stefan/7922901/working/building/REAL250005054141 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054141 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054141/0 /scratch/stefan/7922901/working/building/REAL250005054141 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/263 `/scratch/stefan/7922901/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054141.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054141 none CO[C@H](C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 154, 201, 201, 154, 154, 85, 55, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 154, 85, 85, 55, 55, 20, 20, 20, 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: 816 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054141 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054141 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054141/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054141 Building REAL250005054142 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054142' /scratch/stefan/7922901/working/building/REAL250005054142 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054142 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054142/0 /scratch/stefan/7922901/working/building/REAL250005054142 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/264 `/scratch/stefan/7922901/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005054142.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054142 none CC1=NNC(C(=O)NCCN(C)C(=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.3', '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, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 99, 69, 27, 10, 27, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 99, 99, 69, 69, 27, 27, 27, 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: 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: REAL250005054142 none CC1=NNC(C(=O)NCCN(C)C(=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.3', '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, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 22, 41, 95, 95, 169, 169, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 4, 22, 22, 41, 41, 95, 95, 95, 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: 624 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054142 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054142/1 /scratch/stefan/7922901/working/building/REAL250005054142 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/265 `/scratch/stefan/7922901/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)N1) `REAL250005054142.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054142/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054142 none CC1=NN=C(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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 201 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, 200, 200, 200, 104, 78, 32, 12, 32, 1, 12, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 200, 104, 104, 78, 78, 32, 32, 32, 1, 201] 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, 33]) 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: REAL250005054142 none CC1=NN=C(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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 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, 5, 5, 19, 39, 85, 85, 169, 169, 201, 201, 201, 201, 201, 1, 2, 2, 2, 5, 19, 19, 39, 39, 85, 85, 85, 201, 1] 201 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: 630 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054142 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054142 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054142/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054142/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054142 Building REAL250005054143 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054143' /scratch/stefan/7922901/working/building/REAL250005054143 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054143 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054143/0 /scratch/stefan/7922901/working/building/REAL250005054143 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/266 `/scratch/stefan/7922901/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=COC(=O)N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054143.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054143 none CN(CCNC(=O)C1=COC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 6, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 16, 23, 23, 28, 28, 28, 39, 39, 39, 39, 39, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 23, 23, 23, 23, 28, 39, 39, 1] 39 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: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054143 none CN(CCNC(=O)C1=COC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 6, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [33, 32, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 33, 39, 39, 39, 39, 39, 39, 39, 33, 33, 33, 32, 32, 21, 21, 6, 1, 1, 39] 39 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054143 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054143/1 /scratch/stefan/7922901/working/building/REAL250005054143 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/267 `/scratch/stefan/7922901/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=COC(=O)[N-]1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054143.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054143 none CN(CCNC(=O)C1=COC(=O)[N-]1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [24, 10, 24, 42, 53, 81, 81, 81, 92, 92, 92, 92, 92, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 42, 42, 53, 53, 81, 92, 1] 92 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 313 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: REAL250005054143 none CN(CCNC(=O)C1=COC(=O)[N-]1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [48, 38, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 48, 78, 78, 92, 92, 92, 92, 92, 48, 48, 48, 38, 38, 24, 24, 8, 1, 92] 92 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30]) total number of confs: 306 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054143 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054143 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054143/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054143/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054143 Building REAL250005054144 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054144' /scratch/stefan/7922901/working/building/REAL250005054144 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054144 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054144/0 /scratch/stefan/7922901/working/building/REAL250005054144 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/268 `/scratch/stefan/7922901/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054144.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054144 none CC=CC(O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 507 conformations in input total number of sets (complete confs): 507 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 139, 119, 139, 119, 119, 68, 49, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 169, 139, 417, 119, 68, 68, 49, 49, 17, 17, 17, 1] 507 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: 1097 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054144 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054144 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054144/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054144 Building REAL250005054145 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054145' /scratch/stefan/7922901/working/building/REAL250005054145 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054145 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054145/0 /scratch/stefan/7922901/working/building/REAL250005054145 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/269 `/scratch/stefan/7922901/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054145.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054145 none CCCC[C@H](C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 141, 61, 141, 141, 61, 61, 43, 36, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 175, 175, 175, 175, 141, 141, 141, 61, 43, 43, 36, 36, 16, 16, 16, 1] 175 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: 790 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054145 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054145 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054145/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054145 Building REAL250005054146 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054146' /scratch/stefan/7922901/working/building/REAL250005054146 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054146 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054146/0 /scratch/stefan/7922901/working/building/REAL250005054146 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/270 `/scratch/stefan/7922901/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005054146.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054146 none C[C@@H](C(=O)NCCN(C)C(=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.3', '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, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3] 3 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: 7 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054146 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054146/1 /scratch/stefan/7922901/working/building/REAL250005054146 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/271 `/scratch/stefan/7922901/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)N(C)C) `REAL250005054146.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005054146 none C[C@@H](C(=O)NCCN(C)C(=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.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 137, 156, 137, 137, 90, 63, 28, 11, 28, 1, 11, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 156, 137, 90, 90, 63, 63, 28, 28, 28, 1, 156, 156, 156, 156, 156, 156] 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, 33, 34, 35, 36, 37, 38]) total number of confs: 636 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054146 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054146 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054146/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054146/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054146 Building REAL250005054147 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054147' /scratch/stefan/7922901/working/building/REAL250005054147 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054147 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054147/0 /scratch/stefan/7922901/working/building/REAL250005054147 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/272 `/scratch/stefan/7922901/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054147.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054147 none CCC=C(F)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 125, 125, 93, 125, 93, 93, 57, 39, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 125, 93, 57, 57, 39, 39, 17, 17, 17, 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: 913 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054147 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054147 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054147/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054147 Building REAL250005054148 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054148' /scratch/stefan/7922901/working/building/REAL250005054148 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054148 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054148/0 /scratch/stefan/7922901/working/building/REAL250005054148 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/273 `/scratch/stefan/7922901/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054148.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054148 none CCC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 81, 81, 81, 59, 45, 17, 8, 17, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 131, 131, 81, 59, 59, 45, 45, 17, 17, 17, 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: 927 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054148 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054148 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054148/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054148 Building REAL250005054149 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054149' /scratch/stefan/7922901/working/building/REAL250005054149 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005054149 as failed and skipping /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `/scratch/stefan/7922901/failed' `/scratch/stefan/7922901/working/building/REAL250005054149' -> `/scratch/stefan/7922901/failed/REAL250005054149' Building REAL250005054150 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054150' /scratch/stefan/7922901/working/building/REAL250005054150 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054150 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054150/0 /scratch/stefan/7922901/working/building/REAL250005054150 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/274 `/scratch/stefan/7922901/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCC(=O)N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054150.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054150 none CN(CCNC(=O)C1CCC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 8, 20, 27, 27, 47, 47, 47, 80, 80, 80, 80, 80, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 47, 80, 80, 80, 80, 80, 80, 1] 80 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: 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: REAL250005054150 none CN(CCNC(=O)C1CCC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [65, 58, 43, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 65, 79, 79, 80, 80, 80, 80, 80, 65, 65, 65, 58, 58, 43, 43, 11, 1, 1, 1, 1, 1, 1, 80] 80 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054150 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054150 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054150/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054150 Building REAL250005054151 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054151' /scratch/stefan/7922901/working/building/REAL250005054151 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054151 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054151/0 /scratch/stefan/7922901/working/building/REAL250005054151 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/275 `/scratch/stefan/7922901/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(C)(C)CO)C(=O)C1=CC(=O)[N-]O1) `REAL250005054151.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054151 none CN(CCNC(=O)C(C)(C)CO)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 6, 19, 43, 53, 106, 106, 106, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 43, 43, 53, 53, 106, 201, 201, 201, 201, 201, 201, 201, 201, 603, 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: 1437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054151 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054151 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054151/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054151 Building REAL250005054152 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054152' /scratch/stefan/7922901/working/building/REAL250005054152 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054152 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054152/0 /scratch/stefan/7922901/working/building/REAL250005054152 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/276 `/scratch/stefan/7922901/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NC=CN1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054152.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054152 none CN(CCNC(=O)C1=NC=CN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 6, 16, 25, 25, 45, 45, 45, 67, 67, 67, 67, 67, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 25, 25, 25, 25, 45, 67, 67, 67, 67, 67, 1] 67 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: 191 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: REAL250005054152 none CN(CCNC(=O)C1=NC=CN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [57, 51, 33, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 57, 65, 65, 67, 67, 67, 67, 67, 57, 57, 57, 51, 51, 33, 33, 7, 1, 1, 2, 2, 2, 67] 67 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 281 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054152 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054152 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054152/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054152 Building REAL250005054153 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054153' /scratch/stefan/7922901/working/building/REAL250005054153 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054153 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054153/0 /scratch/stefan/7922901/working/building/REAL250005054153 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/277 `/scratch/stefan/7922901/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC(O)C1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054153.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054153 none CN(CCNC(=O)CC(O)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 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: [16, 6, 16, 31, 35, 62, 62, 62, 148, 164, 164, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 31, 31, 35, 35, 62, 148, 148, 164, 492, 201, 201, 201, 201, 201, 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: 1308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054153 none CN(CCNC(=O)CC(O)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 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: [186, 164, 133, 51, 51, 14, 51, 6, 1, 6, 1, 1, 1, 186, 199, 199, 201, 201, 201, 201, 201, 186, 186, 186, 164, 164, 133, 133, 51, 14, 14, 6, 18, 1, 1, 1, 1, 1, 201] 603 rigid atoms, others: [33, 34, 35, 36, 37, 8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 828 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054153 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054153 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054153/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054153 Building REAL250005054154 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054154' /scratch/stefan/7922901/working/building/REAL250005054154 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054154 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054154/0 /scratch/stefan/7922901/working/building/REAL250005054154 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/278 `/scratch/stefan/7922901/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1CC1)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054154.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054154 none CC(=CC1CC1)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 47, 111, 111, 201, 201, 47, 47, 40, 34, 16, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 201, 201, 201, 201, 201, 47, 40, 40, 34, 34, 16, 16, 16, 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: 723 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: REAL250005054154 none CC(=CC1CC1)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 4, 23, 23, 23, 64, 93, 117, 117, 179, 179, 201, 201, 201, 201, 201, 4, 4, 4, 4, 1, 1, 1, 1, 1, 23, 64, 64, 93, 93, 117, 117, 117, 201] 201 rigid atoms, others: [2, 3, 4, 5, 25, 26, 27, 28, 29] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 755 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054154 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054154 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054154/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054154 Building REAL250005054155 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054155' /scratch/stefan/7922901/working/building/REAL250005054155 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054155 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054155/0 /scratch/stefan/7922901/working/building/REAL250005054155 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/279 `/scratch/stefan/7922901/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCC=CO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054155.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054155 none CN(CCNC(=O)C1CCC=CO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 27, 27, 45, 45, 45, 93, 93, 93, 93, 93, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 45, 93, 93, 93, 93, 93, 93, 93, 1] 93 rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054155 none CN(CCNC(=O)C1CCC=CO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [67, 62, 47, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 67, 93, 93, 93, 93, 93, 93, 93, 67, 67, 67, 62, 62, 47, 47, 13, 1, 1, 1, 1, 1, 1, 1, 93] 93 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054155 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054155 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054155/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054155 Building REAL250005054156 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054156' /scratch/stefan/7922901/working/building/REAL250005054156 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054156 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054156/0 /scratch/stefan/7922901/working/building/REAL250005054156 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/280 `/scratch/stefan/7922901/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1CSC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054156.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054156 none CN(CCNC(=O)CC1CSC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 20, 37, 41, 70, 70, 70, 142, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 37, 37, 41, 41, 70, 142, 142, 201, 201, 201, 201, 201, 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: 851 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: REAL250005054156 none CN(CCNC(=O)CC1CSC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 126, 97, 40, 40, 9, 40, 1, 1, 1, 1, 1, 168, 199, 199, 201, 201, 201, 201, 201, 168, 168, 168, 126, 126, 97, 97, 40, 9, 9, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 792 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054156 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054156 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054156/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054156 Building REAL250005054157 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054157' /scratch/stefan/7922901/working/building/REAL250005054157 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054157 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054157/0 /scratch/stefan/7922901/working/building/REAL250005054157 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/281 `/scratch/stefan/7922901/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(F)CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054157.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054157 none CN(CCNC(=O)C1(F)CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 7, 19, 26, 26, 54, 54, 54, 115, 115, 115, 115, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 26, 26, 26, 26, 54, 115, 115, 115, 115, 115, 115, 1] 115 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: 359 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054157 none CN(CCNC(=O)C1(F)CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [96, 77, 55, 11, 11, 1, 11, 1, 1, 1, 1, 1, 96, 115, 115, 115, 115, 115, 115, 115, 96, 96, 96, 77, 77, 55, 55, 11, 1, 1, 1, 1, 1, 1, 115] 115 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34]) total number of confs: 461 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054157 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054157 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054157/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054157 Building REAL250005054158 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054158' /scratch/stefan/7922901/working/building/REAL250005054158 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054158 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054158/0 /scratch/stefan/7922901/working/building/REAL250005054158 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/282 `/scratch/stefan/7922901/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C=CC(N)=O)C(=O)C1=CC(=O)[N-]O1) `REAL250005054158.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054158 none CN(CCNC(=O)C=CC(N)=O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 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: [17, 6, 17, 31, 35, 57, 57, 57, 83, 83, 95, 95, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 31, 31, 35, 35, 57, 83, 83, 95, 95, 1] 95 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: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054158 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054158 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054158/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054158 Building REAL250005054159 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054159' /scratch/stefan/7922901/working/building/REAL250005054159 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054159 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054159/0 /scratch/stefan/7922901/working/building/REAL250005054159 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/283 `/scratch/stefan/7922901/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCSCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054159.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054159 none C#CCSCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 14, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 148, 101, 58, 58, 58, 46, 40, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 171, 171, 171, 101, 101, 58, 46, 46, 40, 40, 16, 16, 16, 1] 171 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: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054159 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054159 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054159/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054159 Building REAL250005054160 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054160' /scratch/stefan/7922901/working/building/REAL250005054160 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054160 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054160/0 /scratch/stefan/7922901/working/building/REAL250005054160 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/284 `/scratch/stefan/7922901/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054160.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054160 none CC(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 177, 201, 177, 177, 105, 71, 23, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 177, 105, 105, 71, 71, 23, 23, 23, 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: 1411 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054160 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054160 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054160/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054160 Building REAL250005054161 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054161' /scratch/stefan/7922901/working/building/REAL250005054161 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054161 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054161/0 /scratch/stefan/7922901/working/building/REAL250005054161 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/285 `/scratch/stefan/7922901/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(O)CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054161.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054161 none CN(CCNC(=O)C1(O)CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 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 357 conformations in input total number of sets (complete confs): 357 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 22, 34, 34, 75, 75, 75, 119, 119, 119, 119, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 34, 34, 34, 34, 75, 357, 119, 119, 119, 119, 119, 119, 1] 357 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: 744 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054161 none CN(CCNC(=O)C1(O)CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 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 357 conformations in input total number of sets (complete confs): 357 using faster count positions algorithm for large data unique positions, atoms: [98, 85, 55, 11, 11, 1, 11, 1, 1, 1, 1, 1, 98, 119, 119, 119, 119, 119, 119, 119, 98, 98, 98, 85, 85, 55, 55, 11, 6, 1, 1, 1, 1, 1, 1, 119] 357 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 501 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054161 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054161 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054161/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054161 Building REAL250005054162 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054162' /scratch/stefan/7922901/working/building/REAL250005054162 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054162 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054162/0 /scratch/stefan/7922901/working/building/REAL250005054162 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/286 `/scratch/stefan/7922901/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(O)C1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054162.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054162 none CN(CCNC(=O)C(O)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 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 348 conformations in input total number of sets (complete confs): 348 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 26, 26, 50, 50, 50, 105, 105, 116, 116, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 26, 26, 26, 26, 50, 105, 315, 116, 116, 116, 116, 116, 1] 348 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: 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: REAL250005054162 none CN(CCNC(=O)C(O)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 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 348 conformations in input total number of sets (complete confs): 348 using faster count positions algorithm for large data unique positions, atoms: [108, 99, 84, 30, 30, 7, 30, 1, 7, 1, 1, 1, 108, 114, 114, 116, 116, 116, 116, 116, 108, 108, 108, 99, 99, 84, 84, 30, 7, 21, 1, 1, 1, 1, 1, 116] 348 rigid atoms, others: [32, 33, 34, 7, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054162 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054162 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054162/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054162 Building REAL250005054163 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054163' /scratch/stefan/7922901/working/building/REAL250005054163 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054163 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054163/0 /scratch/stefan/7922901/working/building/REAL250005054163 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/287 `/scratch/stefan/7922901/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CN1C=NN=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054163.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054163 none CN(CCNC(=O)CN1C=NN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 8, 22, 33, 33, 81, 81, 81, 186, 200, 200, 200, 200, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 33, 33, 33, 33, 81, 186, 186, 200, 200, 1] 200 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: 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: REAL250005054163 none CN(CCNC(=O)CN1C=NN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 1, 8, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 147, 115, 40, 40, 8, 40, 1, 1, 1, 1, 1, 1, 172, 201, 201, 201, 201, 201, 201, 201, 172, 172, 172, 147, 147, 115, 115, 40, 8, 8, 1, 1, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 817 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054163 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054163 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054163/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054163 Building REAL250005054164 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054164' /scratch/stefan/7922901/working/building/REAL250005054164 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054164 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054164/0 /scratch/stefan/7922901/working/building/REAL250005054164 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/288 `/scratch/stefan/7922901/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054164.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054164 none C=CCC(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 100, 50, 100, 50, 50, 38, 32, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 100, 100, 100, 100, 50, 38, 38, 32, 32, 16, 16, 16, 1] 140 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054164 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054164 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054164/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054164 Building REAL250005054165 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054165' /scratch/stefan/7922901/working/building/REAL250005054165 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054165 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054165/0 /scratch/stefan/7922901/working/building/REAL250005054165 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/289 `/scratch/stefan/7922901/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC1F)C(=O)C1=CC(=O)[N-]O1) `REAL250005054165.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054165 none CN(CCNC(=O)C1CC1F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 5, 5, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [21, 6, 21, 49, 64, 111, 111, 111, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 21, 21, 21, 49, 49, 64, 64, 111, 201, 201, 201, 201, 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: 686 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054165 none CN(CCNC(=O)C1CC1F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 5, 5, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [138, 102, 64, 13, 13, 1, 13, 1, 1, 1, 1, 138, 196, 196, 201, 201, 201, 201, 201, 138, 138, 138, 102, 102, 64, 64, 13, 1, 1, 1, 1, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 798 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054165 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054165 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054165/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054165 Building REAL250005054166 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054166' /scratch/stefan/7922901/working/building/REAL250005054166 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054166 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054166/0 /scratch/stefan/7922901/working/building/REAL250005054166 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/290 `/scratch/stefan/7922901/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005054166.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054166 none C[C@@H](C(=O)NCCN(C)C(=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.3', '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, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3] 3 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: 7 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054166 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054166/1 /scratch/stefan/7922901/working/building/REAL250005054166 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/291 `/scratch/stefan/7922901/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)N(C)C) `REAL250005054166.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005054166 none C[C@@H](C(=O)NCCN(C)C(=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.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 137, 156, 137, 137, 90, 63, 28, 11, 28, 1, 11, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 156, 137, 90, 90, 63, 63, 28, 28, 28, 1, 156, 156, 156, 156, 156, 156] 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, 33, 34, 35, 36, 37, 38]) total number of confs: 636 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054166 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054166 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054166/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054166/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054166 Building REAL250005054167 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054167' /scratch/stefan/7922901/working/building/REAL250005054167 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054167 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054167/0 /scratch/stefan/7922901/working/building/REAL250005054167 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/292 `/scratch/stefan/7922901/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCF)C(=O)C1=CC(=O)[N-]O1) `REAL250005054167.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054167 none CN(CCNC(=O)CCF)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 5, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 22, 46, 59, 98, 98, 98, 192, 201, 1, 6, 1, 1, 1, 1, 1, 1, 22, 22, 22, 46, 46, 59, 59, 98, 192, 192, 201, 201, 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: 839 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054167 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054167 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054167/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054167 Building REAL250005054168 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054168' /scratch/stefan/7922901/working/building/REAL250005054168 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054168 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054168/0 /scratch/stefan/7922901/working/building/REAL250005054168 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/293 `/scratch/stefan/7922901/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CN1C=CN=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054168.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054168 none CN(CCNC(=O)CN1C=CN=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 27, 27, 63, 63, 63, 171, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 63, 171, 171, 201, 201, 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: REAL250005054168 none CN(CCNC(=O)CN1C=CN=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 155, 124, 39, 39, 9, 39, 1, 1, 1, 1, 1, 1, 173, 201, 201, 201, 201, 201, 201, 201, 173, 173, 173, 155, 155, 124, 124, 39, 9, 9, 1, 1, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 803 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054168 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054168 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054168/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054168 Building REAL250005054169 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054169' /scratch/stefan/7922901/working/building/REAL250005054169 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054169 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054169/0 /scratch/stefan/7922901/working/building/REAL250005054169 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/294 `/scratch/stefan/7922901/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005054169.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054169 none C=CC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 105, 105, 68, 54, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 105, 68, 68, 54, 54, 22, 22, 22, 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: 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: REAL250005054169 none C=CC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 28, 53, 86, 86, 161, 161, 201, 201, 201, 201, 201, 1, 1, 1, 5, 5, 5, 6, 28, 28, 53, 53, 86, 86, 86, 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: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054169 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054169 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054169/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054169 Building REAL250005054170 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054170' /scratch/stefan/7922901/working/building/REAL250005054170 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054170 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054170/0 /scratch/stefan/7922901/working/building/REAL250005054170 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/295 `/scratch/stefan/7922901/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(O)COC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054170.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054170 none CN(CCNC(=O)C1(O)COC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 3, 7, 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 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 21, 30, 30, 55, 55, 55, 86, 86, 86, 86, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 30, 30, 30, 30, 55, 258, 86, 86, 86, 86, 1] 258 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: 543 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: REAL250005054170 none CN(CCNC(=O)C1(O)COC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 3, 7, 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 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [72, 58, 41, 12, 12, 1, 12, 1, 1, 1, 1, 1, 72, 85, 85, 86, 86, 86, 86, 86, 72, 72, 72, 58, 58, 41, 41, 12, 6, 1, 1, 1, 1, 86] 258 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 348 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054170 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054170 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054170/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054170 Building REAL250005054171 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054171' /scratch/stefan/7922901/working/building/REAL250005054171 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054171 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054171/0 /scratch/stefan/7922901/working/building/REAL250005054171 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/296 `/scratch/stefan/7922901/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054171.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054171 none CCC(C)C(O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 180, 200, 132, 180, 132, 132, 71, 50, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 200, 200, 180, 540, 132, 71, 71, 50, 50, 19, 19, 19, 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: 1414 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054171 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054171 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054171/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054171 Building REAL250005054172 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054172' /scratch/stefan/7922901/working/building/REAL250005054172 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054172 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054172/0 /scratch/stefan/7922901/working/building/REAL250005054172 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/297 `/scratch/stefan/7922901/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)=C1CC1) `REAL250005054172.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054172 none CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)=C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.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, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 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, 10, 10, 10, 53, 80, 115, 115, 189, 189, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 10, 53, 53, 80, 80, 115, 115, 115, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 17, 18, 19] set([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]) 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: REAL250005054172 none CC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)=C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.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, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 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, 132, 132, 132, 80, 63, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 132, 80, 80, 63, 63, 21, 21, 21, 1, 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]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054172 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054172 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054172/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054172 Building REAL250005054173 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054173' /scratch/stefan/7922901/working/building/REAL250005054173 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054173 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054173/0 /scratch/stefan/7922901/working/building/REAL250005054173 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/298 `/scratch/stefan/7922901/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054173.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054173 none CCC1CC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 144, 144, 144, 79, 62, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 79, 79, 62, 62, 22, 22, 22, 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: 721 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054173 none CCC1CC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 8, 8, 8, 38, 65, 102, 102, 188, 188, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 1, 1, 1, 1, 8, 38, 38, 65, 65, 102, 102, 102, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 25, 26, 27, 28] set([0, 6, 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, 36, 37]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054173 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054173 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054173/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054173 Building REAL250005054174 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054174' /scratch/stefan/7922901/working/building/REAL250005054174 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054174 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054174/0 /scratch/stefan/7922901/working/building/REAL250005054174 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/299 `/scratch/stefan/7922901/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054174.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054174 none CC(O)CCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [55, 58, 58, 54, 51, 29, 29, 29, 28, 22, 12, 5, 12, 1, 5, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 174, 58, 58, 58, 58, 52, 52, 29, 28, 28, 22, 22, 12, 12, 12, 1] 174 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: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054174 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054174 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054174/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054174 Building REAL250005054175 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054175' /scratch/stefan/7922901/working/building/REAL250005054175 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054175 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054175/0 /scratch/stefan/7922901/working/building/REAL250005054175 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/300 `/scratch/stefan/7922901/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1(O)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054175.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054175 none CN(CCNC(=O)CC1(O)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 31, 38, 68, 68, 68, 175, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 31, 31, 38, 38, 68, 175, 175, 603, 201, 201, 201, 201, 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: 1408 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: REAL250005054175 none CN(CCNC(=O)CC1(O)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [179, 147, 118, 33, 33, 8, 33, 1, 1, 1, 1, 1, 179, 201, 201, 201, 201, 201, 201, 201, 179, 179, 179, 147, 147, 118, 118, 33, 8, 8, 6, 1, 1, 1, 1, 201] 603 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 808 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054175 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054175 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054175/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054175 Building REAL250005054176 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054176' /scratch/stefan/7922901/working/building/REAL250005054176 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054176 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054176/0 /scratch/stefan/7922901/working/building/REAL250005054176 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/301 `/scratch/stefan/7922901/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C=CCF)C(=O)C1=CC(=O)[N-]O1) `REAL250005054176.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054176 none CN(CCNC(=O)C=CCF)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'C.2', 'O.2', 'C.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, 5, 8, 1, 11, 1, 1, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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, 6, 17, 45, 59, 100, 100, 100, 170, 170, 201, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 45, 45, 59, 59, 100, 170, 170, 201, 201, 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: 797 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054176 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054176 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054176/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054176 Building REAL250005054177 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054177' /scratch/stefan/7922901/working/building/REAL250005054177 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054177 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054177/0 /scratch/stefan/7922901/working/building/REAL250005054177 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/302 `/scratch/stefan/7922901/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(F)CC1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054177.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054177 none CN(CCNC(=O)C(F)CC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 24, 24, 49, 49, 49, 136, 136, 164, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 24, 24, 24, 24, 49, 136, 166, 166, 201, 201, 201, 201, 201, 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: 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: REAL250005054177 none CN(CCNC(=O)C(F)CC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 183, 167, 71, 71, 14, 71, 3, 14, 1, 1, 1, 1, 188, 200, 200, 201, 201, 201, 201, 201, 188, 188, 188, 183, 183, 167, 167, 71, 14, 3, 3, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37]) total number of confs: 786 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054177 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054177 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054177/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054177 Building REAL250005054178 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054178' /scratch/stefan/7922901/working/building/REAL250005054178 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054178 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054178/0 /scratch/stefan/7922901/working/building/REAL250005054178 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/303 `/scratch/stefan/7922901/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)OC) `REAL250005054178.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054178 none CCC(CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)OC 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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 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, 77, 77, 66, 66, 66, 47, 40, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 77, 78, 78, 78, 78, 78, 78, 77, 77, 77, 66, 47, 47, 40, 40, 14, 14, 14, 1, 78, 78, 78] 78 rigid atoms, others: [37, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 322 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054178 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054178 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054178/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054178 Building REAL250005054179 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054179' /scratch/stefan/7922901/working/building/REAL250005054179 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054179 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054179/0 /scratch/stefan/7922901/working/building/REAL250005054179 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/304 `/scratch/stefan/7922901/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=C(Cl)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054179.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054179 none CN(CCNC(=O)C1=C(Cl)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 10, 24, 52, 73, 121, 121, 121, 187, 187, 187, 187, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 24, 52, 52, 73, 73, 121, 187, 187, 187, 187, 1] 187 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: 558 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054179 none CN(CCNC(=O)C1=C(Cl)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 16, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [120, 87, 57, 13, 13, 1, 13, 1, 1, 1, 1, 1, 120, 182, 182, 187, 187, 187, 187, 187, 120, 120, 120, 87, 87, 57, 57, 13, 1, 1, 1, 1, 187] 187 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054179 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054179 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054179/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054179 Building REAL250005054180 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054180' /scratch/stefan/7922901/working/building/REAL250005054180 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054180 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054180/0 /scratch/stefan/7922901/working/building/REAL250005054180 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/305 `/scratch/stefan/7922901/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]12C[C@H]1[C@H](F)C2)C(=O)C1=CC(=O)[N-]O1) `REAL250005054180.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054180 none CN(CCNC(=O)[C@]12C[C@H]1[C@H](F)C2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'F', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 48, 57, 87, 87, 87, 201, 201, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 48, 48, 57, 57, 87, 201, 201, 201, 201, 1] 201 rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 475 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054180 none CN(CCNC(=O)[C@]12C[C@H]1[C@H](F)C2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'F', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 68, 37, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 111, 190, 190, 201, 201, 201, 201, 201, 111, 111, 111, 68, 68, 37, 37, 7, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054180 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054180 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054180/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054180 Building REAL250005054181 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054181' /scratch/stefan/7922901/working/building/REAL250005054181 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054181 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054181/0 /scratch/stefan/7922901/working/building/REAL250005054181 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/306 `/scratch/stefan/7922901/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CCCOC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054181.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054181 none CN(CCNC(=O)C1=CCCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 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: [22, 7, 22, 50, 60, 95, 95, 95, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 22, 22, 22, 50, 50, 60, 60, 95, 201, 201, 201, 201, 201, 201, 201, 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: 507 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: REAL250005054181 none CN(CCNC(=O)C1=CCCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 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: [127, 94, 61, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 127, 194, 194, 201, 201, 201, 201, 201, 127, 127, 127, 94, 94, 60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 774 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054181 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054181 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054181/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054181 Building REAL250005054182 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054182' /scratch/stefan/7922901/working/building/REAL250005054182 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054182 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054182/0 /scratch/stefan/7922901/working/building/REAL250005054182 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/307 `/scratch/stefan/7922901/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(O)C(C)(C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054182.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054182 none CN(CCNC(=O)C(O)C(C)(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 22, 22, 42, 42, 42, 48, 48, 49, 49, 49, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 16, 22, 22, 22, 22, 42, 48, 144, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1] 147 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: 314 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054182 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054182 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054182/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054182 Building REAL250005054183 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054183' /scratch/stefan/7922901/working/building/REAL250005054183 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054183 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054183/0 /scratch/stefan/7922901/working/building/REAL250005054183 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/308 `/scratch/stefan/7922901/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054183.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054183 none C#CCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 192, 92, 92, 92, 66, 45, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 200, 201, 201, 193, 193, 92, 66, 66, 45, 45, 16, 16, 16, 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: 854 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054183 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054183 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054183/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054183 Building REAL250005054184 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054184' /scratch/stefan/7922901/working/building/REAL250005054184 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054184 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054184/0 /scratch/stefan/7922901/working/building/REAL250005054184 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/309 `/scratch/stefan/7922901/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CN1CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054184.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054184 none CN(CCNC(=O)CN1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 23, 32, 32, 78, 78, 78, 145, 169, 169, 169, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 32, 32, 32, 32, 78, 145, 145, 169, 169, 169, 169, 169, 169, 1] 169 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: 628 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054184 none CN(CCNC(=O)CN1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [141, 123, 99, 34, 34, 7, 34, 1, 1, 1, 1, 1, 141, 168, 168, 169, 169, 169, 169, 169, 141, 141, 141, 123, 123, 99, 99, 34, 7, 7, 1, 1, 1, 1, 1, 1, 169] 169 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054184 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054184/1 /scratch/stefan/7922901/working/building/REAL250005054184 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/310 `/scratch/stefan/7922901/working/3D/310' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C[NH+]1CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054184.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054184 none CN(CCNC(=O)C[NH+]1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 13, 13, 21, 21, 21, 25, 25, 25, 25, 25, 1, 9, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 21, 25, 25, 25, 25, 25, 25, 25, 25, 1] 25 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: 87 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: REAL250005054184 none CN(CCNC(=O)C[NH+]1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 21, 17, 17, 5, 17, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 21, 21, 21, 17, 5, 5, 1, 1, 1, 1, 1, 1, 25] 25 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054184 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054184 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054184/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054184/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054184 Building REAL250005054185 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054185' /scratch/stefan/7922901/working/building/REAL250005054185 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054185 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054185/0 /scratch/stefan/7922901/working/building/REAL250005054185 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/311 `/scratch/stefan/7922901/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(O)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054185.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054185 none CC(C)C(O)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 339 conformations in input total number of sets (complete confs): 339 using faster count positions algorithm for large data unique positions, atoms: [113, 104, 113, 102, 104, 63, 63, 63, 51, 36, 17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 113, 113, 104, 312, 102, 102, 63, 51, 51, 36, 36, 17, 17, 17, 1] 339 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: 814 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054185 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054185 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054185/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054185 Building REAL250005054186 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054186' /scratch/stefan/7922901/working/building/REAL250005054186 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054186 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054186/0 /scratch/stefan/7922901/working/building/REAL250005054186 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/312 `/scratch/stefan/7922901/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054186.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054186 none CCCC(C)(O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 154, 125, 154, 154, 125, 125, 69, 49, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 154, 154, 154, 462, 125, 69, 69, 49, 49, 18, 18, 18, 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: 1362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054186 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054186 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054186/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054186 Building REAL250005054187 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054187' /scratch/stefan/7922901/working/building/REAL250005054187 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054187 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054187/0 /scratch/stefan/7922901/working/building/REAL250005054187 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/313 `/scratch/stefan/7922901/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054187.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054187 none CCOC(C)(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 133, 201, 201, 133, 133, 74, 52, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 74, 74, 52, 52, 16, 16, 16, 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: 858 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054187 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054187 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054187/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054187 Building REAL250005054188 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054188' /scratch/stefan/7922901/working/building/REAL250005054188 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054188 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054188/0 /scratch/stefan/7922901/working/building/REAL250005054188 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/314 `/scratch/stefan/7922901/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#C[C@H]1C[C@H]1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054188.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054188 none C#C[C@H]1C[C@H]1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 142, 201, 142, 142, 83, 63, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 142, 83, 83, 63, 63, 21, 21, 21, 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: 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: REAL250005054188 none C#C[C@H]1C[C@H]1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 8, 8, 8, 41, 62, 109, 109, 187, 187, 201, 201, 201, 201, 201, 1, 1, 1, 8, 41, 41, 62, 62, 109, 109, 109, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054188 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054188 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054188/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054188 Building REAL250005054189 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054189' /scratch/stefan/7922901/working/building/REAL250005054189 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054189 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054189/0 /scratch/stefan/7922901/working/building/REAL250005054189 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/315 `/scratch/stefan/7922901/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(N=[N+]=[N-])CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054189.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054189 none CN(CCNC(=O)C1(N=[N+]=[N-])CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 8, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 31, 32, 62, 62, 62, 150, 201, 201, 150, 150, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 31, 31, 32, 32, 62, 150, 150, 150, 150, 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: 547 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: REAL250005054189 none CN(CCNC(=O)C1(N=[N+]=[N-])CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 8, 8, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 93, 64, 13, 13, 1, 13, 1, 1, 12, 12, 1, 1, 119, 143, 143, 150, 150, 150, 150, 150, 119, 119, 119, 93, 93, 64, 64, 13, 1, 1, 1, 1, 150] 201 rigid atoms, others: [32, 5, 7, 8, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 598 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054189 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054189 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054189/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054189 Building REAL250005054190 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054190' /scratch/stefan/7922901/working/building/REAL250005054190 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054190 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054190/0 /scratch/stefan/7922901/working/building/REAL250005054190 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/316 `/scratch/stefan/7922901/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CNC(=O)O1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054190.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054190 none CN(CCNC(=O)C1=CNC(=O)O1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 3, 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: [20, 8, 20, 37, 43, 59, 59, 59, 83, 83, 83, 83, 83, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 37, 37, 43, 43, 59, 83, 83, 1] 83 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: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054190 none CN(CCNC(=O)C1=CNC(=O)O1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 3, 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: [59, 41, 29, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 59, 81, 81, 83, 83, 83, 83, 83, 59, 59, 59, 41, 41, 29, 29, 9, 1, 1, 83] 83 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054190 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054190 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054190/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054190 Building REAL250005054191 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054191' /scratch/stefan/7922901/working/building/REAL250005054191 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054191 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054191/0 /scratch/stefan/7922901/working/building/REAL250005054191 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/317 `/scratch/stefan/7922901/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1C[C@H]1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054191.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054191 none CC(C)[C@@H]1C[C@H]1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 80, 201, 80, 80, 55, 44, 16, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 55, 55, 44, 44, 16, 16, 16, 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: 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: REAL250005054191 none CC(C)[C@@H]1C[C@H]1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 13, 13, 13, 52, 80, 112, 112, 180, 180, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 4, 4, 1, 1, 13, 52, 52, 80, 80, 112, 112, 112, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 743 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054191 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054191 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054191/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054191 Building REAL250005054192 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054192' /scratch/stefan/7922901/working/building/REAL250005054192 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054192 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054192/0 /scratch/stefan/7922901/working/building/REAL250005054192 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/318 `/scratch/stefan/7922901/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1C2CCC21)C(=O)C1=CC(=O)[N-]O1) `REAL250005054192.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054192 none CN(CCNC(=O)C1C2CCC21)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 10, 27, 69, 93, 161, 161, 161, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 69, 69, 93, 93, 161, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005054192 none CN(CCNC(=O)C1C2CCC21)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 65, 41, 9, 9, 1, 9, 1, 1, 1, 1, 1, 95, 183, 183, 201, 201, 201, 201, 201, 95, 95, 95, 65, 65, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35]) total number of confs: 669 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054192 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054192 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054192/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054192 Building REAL250005054193 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054193' /scratch/stefan/7922901/working/building/REAL250005054193 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054193 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054193/0 /scratch/stefan/7922901/working/building/REAL250005054193 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/319 `/scratch/stefan/7922901/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054193.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054193 none C=C1CCC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 145, 145, 145, 91, 62, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 145, 91, 91, 62, 62, 22, 22, 22, 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: 745 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: REAL250005054193 none C=C1CCC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 74, 118, 118, 186, 186, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 10, 44, 44, 74, 74, 118, 118, 118, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 728 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054193 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054193 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054193/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054193 Building REAL250005054194 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054194' /scratch/stefan/7922901/working/building/REAL250005054194 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054194 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054194/0 /scratch/stefan/7922901/working/building/REAL250005054194 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/320 `/scratch/stefan/7922901/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)[C@H]1C) `REAL250005054194.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054194 none C[C@H]1C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 93, 93, 93, 59, 45, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 93, 59, 59, 45, 45, 18, 18, 18, 1, 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]) total number of confs: 685 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: REAL250005054194 none C[C@H]1C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 77, 117, 117, 190, 190, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 13, 45, 45, 77, 77, 117, 117, 117, 201, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 753 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054194 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054194 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054194/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054194 Building REAL250005054195 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054195' /scratch/stefan/7922901/working/building/REAL250005054195 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054195 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054195/0 /scratch/stefan/7922901/working/building/REAL250005054195 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/321 `/scratch/stefan/7922901/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005054195.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054195 none C[C@H](C(=O)NCCN(C)C(=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.3', '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, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3] 3 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: 7 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054195 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054195/1 /scratch/stefan/7922901/working/building/REAL250005054195 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/322 `/scratch/stefan/7922901/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)N(C)C) `REAL250005054195.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005054195 none C[C@H](C(=O)NCCN(C)C(=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.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 10, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 162, 188, 162, 162, 104, 76, 30, 10, 30, 1, 10, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 188, 162, 104, 104, 76, 76, 30, 30, 30, 1, 188, 188, 188, 188, 188, 188] 188 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: 787 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054195 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054195 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054195/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054195/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054195 Building REAL250005054196 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054196' /scratch/stefan/7922901/working/building/REAL250005054196 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054196 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054196/0 /scratch/stefan/7922901/working/building/REAL250005054196 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/323 `/scratch/stefan/7922901/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054196.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054196 none CC=CC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 189, 189, 116, 116, 116, 72, 55, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 189, 116, 72, 72, 55, 55, 20, 20, 20, 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: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054196 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054196 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054196/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054196 Building REAL250005054197 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054197' /scratch/stefan/7922901/working/building/REAL250005054197 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054197 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054197/0 /scratch/stefan/7922901/working/building/REAL250005054197 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/324 `/scratch/stefan/7922901/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NC=NN1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054197.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054197 none CN(CCNC(=O)C1=NC=NN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 5, 13, 25, 25, 45, 45, 45, 63, 63, 63, 63, 63, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 25, 25, 25, 25, 45, 63, 63, 63, 63, 1] 63 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: 185 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: REAL250005054197 none CN(CCNC(=O)C1=NC=NN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 1, 8, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [51, 43, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 51, 61, 61, 63, 63, 63, 63, 63, 51, 51, 51, 43, 43, 30, 30, 8, 1, 2, 2, 2, 63] 63 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 256 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054197 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054197 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054197/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054197 Building REAL250005054198 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054198' /scratch/stefan/7922901/working/building/REAL250005054198 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054198 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054198/0 /scratch/stefan/7922901/working/building/REAL250005054198 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/325 `/scratch/stefan/7922901/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1CC[C@@H](O)C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054198.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054198 none CN(CCNC(=O)[C@@H]1CC[C@@H](O)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 1, 1, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 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 543 conformations in input total number of sets (complete confs): 543 using faster count positions algorithm for large data unique positions, atoms: [26, 9, 26, 47, 58, 95, 95, 95, 181, 181, 181, 181, 181, 181, 181, 1, 9, 1, 1, 1, 1, 1, 1, 24, 26, 26, 47, 47, 58, 58, 95, 181, 181, 181, 181, 543, 181, 181, 1] 543 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: 1141 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: REAL250005054198 none CN(CCNC(=O)[C@@H]1CC[C@@H](O)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 1, 11, 1, 1, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 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 543 conformations in input total number of sets (complete confs): 543 using faster count positions algorithm for large data unique positions, atoms: [111, 80, 49, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 111, 172, 172, 181, 181, 181, 181, 181, 111, 111, 111, 80, 80, 49, 49, 10, 1, 1, 1, 1, 6, 1, 1, 181] 543 rigid atoms, others: [32, 33, 34, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 37, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 38]) total number of confs: 702 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054198 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054198 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054198/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054198 Building REAL250005054199 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054199' /scratch/stefan/7922901/working/building/REAL250005054199 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054199 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054199/0 /scratch/stefan/7922901/working/building/REAL250005054199 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/326 `/scratch/stefan/7922901/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1CC=CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054199.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054199 none CN(CCNC(=O)[C@@H]1CC=CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 22, 49, 59, 97, 97, 97, 201, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 22, 22, 22, 49, 49, 59, 59, 97, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 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: REAL250005054199 none CN(CCNC(=O)[C@@H]1CC=CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 87, 52, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 126, 192, 192, 201, 201, 201, 201, 201, 126, 126, 126, 87, 87, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38]) total number of confs: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054199 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054199 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054199/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054199 Building REAL250005054200 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054200' /scratch/stefan/7922901/working/building/REAL250005054200 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054200 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054200/0 /scratch/stefan/7922901/working/building/REAL250005054200 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/327 `/scratch/stefan/7922901/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054200.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054200 none COCC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 79, 79, 39, 39, 39, 25, 23, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 183, 183, 79, 79, 39, 25, 25, 23, 23, 15, 15, 15, 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: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054200 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054200 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054200/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054200 Building REAL250005054201 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054201' /scratch/stefan/7922901/working/building/REAL250005054201 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054201 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054201/0 /scratch/stefan/7922901/working/building/REAL250005054201 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/328 `/scratch/stefan/7922901/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(CC(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054201.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054201 none CC1CN(CC(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 134, 134, 134, 73, 50, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 200, 200, 134, 73, 73, 50, 50, 17, 17, 17, 1, 201, 201] 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: 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: REAL250005054201 none CC1CN(CC(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 17, 17, 17, 55, 85, 139, 139, 195, 195, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 6, 6, 17, 55, 55, 85, 85, 139, 139, 139, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 38, 39, 20, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054201 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054201/1 /scratch/stefan/7922901/working/building/REAL250005054201 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/329 `/scratch/stefan/7922901/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C[NH+](CC(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054201.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054201 none CC1C[NH+](CC(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 17, 12, 12, 12, 10, 10, 8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 15, 15, 12, 10, 10, 10, 10, 8, 8, 8, 1, 17, 17] 17 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: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054201 none CC1C[NH+](CC(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 9, 9, 9, 14, 14, 14, 14, 15, 15, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1, 1, 1, 4, 4, 9, 14, 14, 14, 14, 14, 14, 14, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 40, 21, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054201 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054201 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054201/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054201/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054201 Building REAL250005054202 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054202' /scratch/stefan/7922901/working/building/REAL250005054202 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054202 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054202/0 /scratch/stefan/7922901/working/building/REAL250005054202 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/330 `/scratch/stefan/7922901/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(C)COC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054202.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054202 none CN(CCNC(=O)C1(C)COC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 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 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 45, 48, 69, 69, 69, 153, 153, 153, 153, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 45, 45, 48, 48, 69, 153, 153, 153, 153, 153, 153, 153, 1] 153 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: 485 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: REAL250005054202 none CN(CCNC(=O)C1(C)COC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 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 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [90, 56, 32, 6, 6, 1, 6, 1, 1, 1, 1, 1, 90, 146, 146, 153, 153, 153, 153, 153, 90, 90, 90, 56, 56, 32, 32, 6, 2, 2, 2, 1, 1, 1, 1, 153] 153 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 574 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054202 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054202 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054202/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054202 Building REAL250005054203 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054203' /scratch/stefan/7922901/working/building/REAL250005054203 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054203 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054203/0 /scratch/stefan/7922901/working/building/REAL250005054203 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/331 `/scratch/stefan/7922901/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CCCCO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054203.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054203 none CN(CCNC(=O)C1=CCCCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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, 19, 43, 49, 111, 111, 111, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 43, 43, 49, 49, 111, 201, 201, 201, 201, 201, 201, 201, 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: 507 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: REAL250005054203 none CN(CCNC(=O)C1=CCCCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 88, 55, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 131, 193, 193, 201, 201, 201, 201, 201, 131, 131, 131, 88, 88, 55, 55, 12, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 771 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054203 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054203 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054203/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054203 Building REAL250005054204 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054204' /scratch/stefan/7922901/working/building/REAL250005054204 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054204 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054204/0 /scratch/stefan/7922901/working/building/REAL250005054204 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/332 `/scratch/stefan/7922901/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CCCS1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054204.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054204 none CN(CCNC(=O)C1=CCCS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 8, 26, 52, 58, 95, 95, 95, 140, 140, 140, 140, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 26, 52, 52, 58, 58, 95, 140, 140, 140, 140, 140, 1] 140 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: 430 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054204 none CN(CCNC(=O)C1=CCCS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [102, 63, 43, 10, 10, 1, 10, 1, 1, 1, 1, 1, 102, 136, 136, 140, 140, 140, 140, 140, 102, 102, 102, 63, 63, 42, 42, 10, 1, 1, 1, 1, 1, 140] 140 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33]) total number of confs: 533 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054204 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054204 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054204/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054204 Building REAL250005054205 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054205' /scratch/stefan/7922901/working/building/REAL250005054205 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054205 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054205/0 /scratch/stefan/7922901/working/building/REAL250005054205 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/333 `/scratch/stefan/7922901/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054205.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054205 none CC1=NOC(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 152, 152, 152, 83, 59, 25, 11, 25, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 152, 83, 83, 59, 59, 25, 25, 25, 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: 705 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: REAL250005054205 none CC1=NOC(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 50, 82, 127, 127, 185, 185, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 11, 50, 50, 82, 82, 127, 127, 127, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 35, 20, 21, 22, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 743 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054205 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054205 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054205/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054205 Building REAL250005054206 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054206' /scratch/stefan/7922901/working/building/REAL250005054206 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054206 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054206/0 /scratch/stefan/7922901/working/building/REAL250005054206 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/334 `/scratch/stefan/7922901/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(=O)NC1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054206.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054206 none CN(CCNC(=O)C(=O)NC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 9, 9, 17, 17, 17, 21, 21, 21, 27, 27, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 17, 21, 27, 27, 27, 27, 27, 1] 27 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: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054206 none CN(CCNC(=O)C(=O)NC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 25, 13, 13, 5, 17, 5, 5, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 26, 26, 25, 25, 17, 5, 1, 1, 1, 1, 1, 27] 27 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054206 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054206 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054206/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054206 Building REAL250005054207 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054207' /scratch/stefan/7922901/working/building/REAL250005054207 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054207 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054207/0 /scratch/stefan/7922901/working/building/REAL250005054207 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/335 `/scratch/stefan/7922901/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCSC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054207.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054207 none CN(CCNC(=O)C1CCSC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 57, 71, 122, 122, 122, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 57, 57, 71, 71, 122, 201, 201, 201, 201, 201, 201, 201, 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: 691 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: REAL250005054207 none CN(CCNC(=O)C1CCSC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 82, 46, 9, 9, 1, 9, 1, 1, 1, 1, 1, 121, 191, 191, 201, 201, 201, 201, 201, 121, 121, 121, 82, 82, 46, 46, 9, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35]) total number of confs: 756 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054207 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054207 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054207/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054207 Building REAL250005054208 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054208' /scratch/stefan/7922901/working/building/REAL250005054208 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054208 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054208/0 /scratch/stefan/7922901/working/building/REAL250005054208 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/336 `/scratch/stefan/7922901/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054208.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054208 none CN(CCNC(=O)C1CCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 32, 32, 59, 59, 59, 115, 115, 115, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 32, 32, 32, 32, 59, 115, 115, 115, 115, 115, 1] 115 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: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054208 none CN(CCNC(=O)C1CCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [88, 69, 47, 10, 10, 1, 10, 1, 1, 1, 1, 88, 111, 111, 115, 115, 115, 115, 115, 88, 88, 88, 69, 69, 47, 47, 10, 1, 1, 1, 1, 1, 115] 115 rigid atoms, others: [5, 7, 8, 9, 10, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054208 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054208 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054208/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054208 Building REAL250005054209 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054209' /scratch/stefan/7922901/working/building/REAL250005054209 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054209 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054209/0 /scratch/stefan/7922901/working/building/REAL250005054209 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/337 `/scratch/stefan/7922901/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCN=[N+]=[N-])C(=O)C1=CC(=O)[N-]O1) `REAL250005054209.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054209 none CN(CCNC(=O)CCN=[N+]=[N-])C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 8, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 15, 25, 29, 49, 49, 49, 137, 155, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 25, 25, 29, 29, 49, 137, 137, 155, 155, 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: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054209 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054209 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054209/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054209 Building REAL250005054210 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054210' /scratch/stefan/7922901/working/building/REAL250005054210 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054210 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054210/0 /scratch/stefan/7922901/working/building/REAL250005054210 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/338 `/scratch/stefan/7922901/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054210.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054210 none C#CCOCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 168, 122, 72, 72, 72, 56, 45, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 122, 122, 72, 56, 56, 45, 45, 18, 18, 18, 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: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054210 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054210 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054210/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054210 Building REAL250005054211 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054211' /scratch/stefan/7922901/working/building/REAL250005054211 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054211 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054211/0 /scratch/stefan/7922901/working/building/REAL250005054211 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/339 `/scratch/stefan/7922901/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1=NN=CO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054211.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054211 none CN(CCNC(=O)CC1=NN=CO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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, 6, 15, 23, 23, 49, 49, 49, 151, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 23, 23, 23, 23, 49, 151, 151, 201, 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: 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: REAL250005054211 none CN(CCNC(=O)CC1=NN=CO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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: [167, 148, 115, 31, 31, 4, 31, 1, 1, 1, 1, 1, 1, 167, 201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 148, 148, 115, 115, 31, 4, 4, 1, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32]) total number of confs: 813 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054211 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054211 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054211/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054211 Building REAL250005054212 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054212' /scratch/stefan/7922901/working/building/REAL250005054212 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054212 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054212/0 /scratch/stefan/7922901/working/building/REAL250005054212 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/340 `/scratch/stefan/7922901/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCCS1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054212.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054212 none CN(CCNC(=O)C1CCCS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 32, 32, 59, 59, 59, 98, 98, 98, 98, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 32, 32, 32, 32, 59, 98, 98, 98, 98, 98, 98, 98, 1] 98 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: 333 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: REAL250005054212 none CN(CCNC(=O)C1CCCS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [76, 60, 44, 12, 12, 1, 12, 1, 1, 1, 1, 1, 76, 94, 94, 98, 98, 98, 98, 98, 76, 76, 76, 60, 60, 44, 44, 12, 1, 1, 1, 1, 1, 1, 1, 98] 98 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35]) total number of confs: 378 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054212 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054212 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054212/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054212 Building REAL250005054213 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054213' /scratch/stefan/7922901/working/building/REAL250005054213 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054213 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054213/0 /scratch/stefan/7922901/working/building/REAL250005054213 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/341 `/scratch/stefan/7922901/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(C)(C)O)C(=O)C1=CC(=O)[N-]O1) `REAL250005054213.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054213 none CN(CCNC(=O)C(C)(C)O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 267 conformations in input total number of sets (complete confs): 267 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 27, 27, 45, 45, 45, 89, 89, 89, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 45, 89, 89, 89, 89, 89, 89, 267, 1] 267 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: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054213 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054213 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054213/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054213 Building REAL250005054214 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054214' /scratch/stefan/7922901/working/building/REAL250005054214 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054214 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054214/0 /scratch/stefan/7922901/working/building/REAL250005054214 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/342 `/scratch/stefan/7922901/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054214.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054214 none CC1=CC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 91, 91, 91, 61, 49, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 91, 61, 61, 49, 49, 18, 18, 18, 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: 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: REAL250005054214 none CC1=CC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 91, 131, 131, 193, 193, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 13, 56, 56, 91, 91, 131, 131, 131, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 781 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054214 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054214 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054214/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054214 Building REAL250005054215 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054215' /scratch/stefan/7922901/working/building/REAL250005054215 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054215 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054215/0 /scratch/stefan/7922901/working/building/REAL250005054215 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/343 `/scratch/stefan/7922901/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054215.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054215 none CN(C)C(=O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 159, 201, 159, 159, 100, 76, 28, 10, 28, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 159, 100, 100, 76, 76, 28, 28, 28, 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: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054215 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054215 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054215/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054215 Building REAL250005054216 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054216' /scratch/stefan/7922901/working/building/REAL250005054216 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054216 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054216/0 /scratch/stefan/7922901/working/building/REAL250005054216 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/344 `/scratch/stefan/7922901/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054216.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054216 none CSC=CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 153, 87, 87, 87, 64, 48, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 153, 153, 87, 64, 64, 48, 48, 19, 19, 19, 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: 626 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054216 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054216 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054216/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054216 Building REAL250005054217 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054217' /scratch/stefan/7922901/working/building/REAL250005054217 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054217 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054217/0 /scratch/stefan/7922901/working/building/REAL250005054217 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/345 `/scratch/stefan/7922901/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054217.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054217 none CCC(C)(O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [200, 177, 117, 177, 177, 117, 117, 59, 48, 19, 10, 19, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 177, 177, 177, 531, 117, 59, 59, 48, 48, 19, 19, 19, 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: 1386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054217 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054217 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054217/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054217 Building REAL250005054218 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054218' /scratch/stefan/7922901/working/building/REAL250005054218 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005054218 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054218/0 /scratch/stefan/7922901/working/building/REAL250005054218 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/346 `/scratch/stefan/7922901/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054218.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054218 none CC[N@H+](C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 21, 23, 23, 19, 19, 19, 11, 11, 9, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 21, 21, 19, 11, 11, 11, 11, 9, 9, 9, 1] 23 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: 85 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054218 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054218/1 /scratch/stefan/7922901/working/building/REAL250005054218 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/347 `/scratch/stefan/7922901/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054218.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005054218 none CC[N@@H+](C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 19, 21, 21, 18, 18, 18, 9, 9, 7, 6, 7, 1, 6, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 19, 19, 18, 9, 9, 9, 9, 7, 7, 7, 1] 21 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: 73 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054218 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `2' /scratch/stefan/7922901/working/building/REAL250005054218/2 /scratch/stefan/7922901/working/building/REAL250005054218 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 2 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/348 `/scratch/stefan/7922901/working/3D/348' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054218.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005054218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054218/2/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: REAL250005054218 none CCN(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 192, 193, 140, 140, 140, 78, 52, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 193, 192, 192, 140, 78, 78, 52, 52, 17, 17, 17, 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: 899 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054218 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054218 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054218/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054218/1.* 2: /scratch/stefan/7922901/working/building/REAL250005054218/2.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054218 Building REAL250005054219 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054219' /scratch/stefan/7922901/working/building/REAL250005054219 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054219 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054219/0 /scratch/stefan/7922901/working/building/REAL250005054219 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/349 `/scratch/stefan/7922901/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054219.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054219 none CCC=CC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 119, 119, 119, 119, 61, 61, 61, 59, 41, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 119, 119, 119, 119, 61, 59, 59, 41, 41, 16, 16, 16, 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: 951 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054219 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054219 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054219/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054219 Building REAL250005054220 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054220' /scratch/stefan/7922901/working/building/REAL250005054220 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054220 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054220/0 /scratch/stefan/7922901/working/building/REAL250005054220 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/350 `/scratch/stefan/7922901/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)N[N-]1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054220.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054220 none CN(CCNC(=O)C1=CC(=O)N[N-]1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [25, 10, 25, 45, 55, 83, 83, 83, 99, 99, 99, 99, 99, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 45, 45, 55, 55, 83, 99, 99, 1] 99 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: 335 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: REAL250005054220 none CN(CCNC(=O)C1=CC(=O)N[N-]1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [47, 37, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 47, 81, 81, 99, 99, 99, 99, 99, 47, 47, 47, 37, 37, 26, 26, 7, 1, 1, 99] 99 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 318 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054220 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054220 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054220/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054220 Building REAL250005054221 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054221' /scratch/stefan/7922901/working/building/REAL250005054221 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054221 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054221/0 /scratch/stefan/7922901/working/building/REAL250005054221 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/351 `/scratch/stefan/7922901/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)=CN1) `REAL250005054221.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054221 none CC1=CC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)=CN1 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.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 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, 116, 116, 116, 87, 65, 21, 10, 21, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 116, 87, 87, 65, 65, 21, 21, 21, 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: 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: REAL250005054221 none CC1=CC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)=CN1 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.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 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, 5, 5, 5, 29, 55, 100, 100, 176, 176, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 5, 29, 29, 55, 55, 100, 100, 100, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 35, 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: 691 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054221 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054221 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054221/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054221 Building REAL250005054222 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054222' /scratch/stefan/7922901/working/building/REAL250005054222 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054222 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054222/0 /scratch/stefan/7922901/working/building/REAL250005054222 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/352 `/scratch/stefan/7922901/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005054222.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054222 none CC1=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCC1 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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 109, 109, 109, 65, 50, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 109, 65, 65, 50, 50, 16, 16, 16, 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: 556 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054222 none CC1=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCC1 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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 73, 109, 109, 190, 190, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 9, 43, 43, 73, 73, 109, 109, 109, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 33, 34, 18, 19, 20, 38] 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: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054222 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054222 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054222/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054222 Building REAL250005054223 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054223' /scratch/stefan/7922901/working/building/REAL250005054223 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054223 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054223/0 /scratch/stefan/7922901/working/building/REAL250005054223 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/353 `/scratch/stefan/7922901/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054223.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054223 none C=C1CC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 88, 88, 88, 57, 45, 18, 8, 18, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 88, 57, 57, 45, 45, 18, 18, 18, 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: 691 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054223 none C=C1CC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 10, 10, 10, 42, 72, 118, 118, 193, 193, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 10, 42, 42, 72, 72, 118, 118, 118, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 19, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 755 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054223 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054223 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054223/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054223 Building REAL250005054224 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054224' /scratch/stefan/7922901/working/building/REAL250005054224 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054224 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054224/0 /scratch/stefan/7922901/working/building/REAL250005054224 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/354 `/scratch/stefan/7922901/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(C)(O)C1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054224.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054224 none CN(CCNC(=O)C(C)(O)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 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 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 20, 20, 38, 38, 38, 61, 61, 61, 66, 66, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 20, 20, 20, 20, 38, 61, 61, 61, 183, 66, 66, 66, 66, 66, 1] 198 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: 438 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: REAL250005054224 none CN(CCNC(=O)C(C)(O)C1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 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 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [60, 54, 47, 21, 21, 7, 21, 1, 7, 7, 1, 1, 1, 60, 66, 66, 66, 66, 66, 66, 66, 60, 60, 60, 54, 54, 47, 47, 21, 7, 7, 7, 21, 1, 1, 1, 1, 1, 66] 198 rigid atoms, others: [33, 34, 35, 36, 37, 7, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 273 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054224 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054224 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054224/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054224 Building REAL250005054225 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054225' /scratch/stefan/7922901/working/building/REAL250005054225 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054225 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054225/0 /scratch/stefan/7922901/working/building/REAL250005054225 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/355 `/scratch/stefan/7922901/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)O1) `REAL250005054225.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054225 none CC1=NC=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)O1 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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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 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, 146, 138, 138, 138, 86, 64, 25, 8, 25, 1, 8, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 146, 138, 86, 86, 64, 64, 25, 25, 25, 1] 146 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: 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: REAL250005054225 none CC1=NC=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)O1 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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 24, 39, 71, 71, 132, 132, 146, 146, 146, 146, 146, 1, 2, 2, 2, 1, 6, 24, 24, 39, 39, 71, 71, 71, 146] 146 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: 490 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054225 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054225 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054225/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054225 Building REAL250005054226 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054226' /scratch/stefan/7922901/working/building/REAL250005054226 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054226 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054226/0 /scratch/stefan/7922901/working/building/REAL250005054226 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/356 `/scratch/stefan/7922901/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCC1F)C(=O)C1=CC(=O)[N-]O1) `REAL250005054226.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054226 none CN(CCNC(=O)C1CCC1F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 28, 57, 77, 110, 110, 110, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 57, 57, 77, 77, 110, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005054226 none CN(CCNC(=O)C1CCC1F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 87, 53, 11, 11, 1, 11, 1, 1, 1, 1, 1, 131, 193, 193, 201, 201, 201, 201, 201, 131, 131, 131, 87, 87, 53, 53, 11, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34]) total number of confs: 777 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054226 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054226 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054226/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054226 Building REAL250005054227 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054227' /scratch/stefan/7922901/working/building/REAL250005054227 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054227 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054227/0 /scratch/stefan/7922901/working/building/REAL250005054227 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/357 `/scratch/stefan/7922901/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CN=CN1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054227.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054227 none CN(CCNC(=O)C1=CN=CN1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 17, 17, 19, 19, 19, 19, 19, 19, 19, 1, 8, 1, 1, 1, 1, 1, 1, 10, 10, 10, 17, 17, 17, 17, 19, 19, 19, 19, 1] 19 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: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054227 none CN(CCNC(=O)C1=CN=CN1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 19, 19, 19, 19, 19, 19, 19, 15, 15, 15, 13, 13, 7, 7, 1, 1, 1, 1, 19] 19 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054227 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054227 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054227/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054227 Building REAL250005054228 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054228' /scratch/stefan/7922901/working/building/REAL250005054228 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054228 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054228/0 /scratch/stefan/7922901/working/building/REAL250005054228 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/358 `/scratch/stefan/7922901/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005054228.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054228 none CC1=NOC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)=N1 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.3', '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, 1, 8, 12, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 173, 173, 173, 102, 76, 30, 10, 30, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 173, 102, 102, 76, 76, 30, 30, 30, 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: 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: REAL250005054228 none CC1=NOC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)=N1 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.3', '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, 1, 8, 12, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 6, 6, 6, 30, 51, 92, 92, 178, 178, 201, 201, 201, 201, 201, 1, 2, 2, 2, 6, 29, 29, 51, 51, 92, 92, 92, 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: 682 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054228 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054228 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054228/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054228 Building REAL250005054229 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054229' /scratch/stefan/7922901/working/building/REAL250005054229 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054229 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054229/0 /scratch/stefan/7922901/working/building/REAL250005054229 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/359 `/scratch/stefan/7922901/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC2CC2C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054229.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054229 none CN(CCNC(=O)C1CC2CC2C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 22, 49, 57, 100, 100, 100, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 49, 49, 57, 57, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 657 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: REAL250005054229 none CN(CCNC(=O)C1CC2CC2C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 73, 46, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 117, 193, 193, 201, 201, 201, 201, 201, 117, 117, 117, 73, 73, 46, 46, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38]) total number of confs: 749 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054229 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054229 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054229/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054229 Building REAL250005054230 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054230' /scratch/stefan/7922901/working/building/REAL250005054230 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054230 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054230/0 /scratch/stefan/7922901/working/building/REAL250005054230 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/360 `/scratch/stefan/7922901/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CCSC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054230.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054230 none CN(CCNC(=O)C1=CCSC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 14, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 10, 29, 69, 82, 120, 120, 120, 176, 176, 176, 176, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 69, 69, 82, 82, 120, 176, 176, 176, 176, 176, 1] 176 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: 541 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054230 none CN(CCNC(=O)C1=CCSC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 14, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [115, 78, 52, 13, 13, 1, 13, 1, 1, 1, 1, 1, 115, 165, 165, 176, 176, 176, 176, 176, 115, 115, 115, 78, 78, 52, 52, 13, 1, 1, 1, 1, 1, 176] 176 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33]) total number of confs: 643 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054230 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054230 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054230/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054230 Building REAL250005054231 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054231' /scratch/stefan/7922901/working/building/REAL250005054231 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054231 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054231/0 /scratch/stefan/7922901/working/building/REAL250005054231 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/361 `/scratch/stefan/7922901/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054231.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054231 none CCCC(O)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 261 conformations in input total number of sets (complete confs): 261 using faster count positions algorithm for large data unique positions, atoms: [86, 87, 81, 73, 82, 46, 46, 46, 40, 30, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 87, 82, 246, 73, 73, 46, 40, 40, 30, 30, 14, 14, 14, 1] 261 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: 667 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054231 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054231 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054231/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054231 Building REAL250005054232 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054232' /scratch/stefan/7922901/working/building/REAL250005054232 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054232 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054232/0 /scratch/stefan/7922901/working/building/REAL250005054232 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/362 `/scratch/stefan/7922901/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(Cl)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054232.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054232 none CN(CCNC(=O)C1(Cl)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 16, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 19, 32, 34, 70, 70, 70, 128, 128, 128, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 32, 32, 34, 34, 70, 128, 128, 128, 128, 1] 128 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: 401 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: REAL250005054232 none CN(CCNC(=O)C1(Cl)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 16, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [101, 79, 56, 12, 12, 1, 12, 1, 1, 1, 1, 101, 124, 124, 128, 128, 128, 128, 128, 101, 101, 101, 79, 79, 56, 56, 12, 1, 1, 1, 1, 128] 128 rigid atoms, others: [5, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 504 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054232 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054232 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054232/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054232 Building REAL250005054233 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054233' /scratch/stefan/7922901/working/building/REAL250005054233 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054233 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054233/0 /scratch/stefan/7922901/working/building/REAL250005054233 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/363 `/scratch/stefan/7922901/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CCCO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054233.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054233 none CN(CCNC(=O)C1=CCCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 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: [25, 10, 25, 52, 62, 103, 103, 103, 157, 157, 157, 157, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 52, 52, 62, 62, 103, 157, 157, 157, 157, 157, 1] 157 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: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054233 none CN(CCNC(=O)C1=CCCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 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: [105, 72, 45, 11, 11, 1, 11, 1, 1, 1, 1, 1, 105, 150, 150, 157, 157, 157, 157, 157, 105, 105, 105, 72, 72, 45, 45, 11, 1, 1, 1, 1, 1, 157] 157 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054233 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054233 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054233/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054233 Building REAL250005054234 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054234' /scratch/stefan/7922901/working/building/REAL250005054234 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054234 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054234/0 /scratch/stefan/7922901/working/building/REAL250005054234 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/364 `/scratch/stefan/7922901/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C=CC[NH+](C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054234.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054234 none CN(CCNC(=O)C=CC[NH+](C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [27, 11, 27, 27, 27, 49, 49, 49, 67, 67, 71, 71, 71, 71, 1, 11, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 49, 67, 67, 71, 71, 71, 71, 71, 71, 71, 71, 1] 71 rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 235 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054234 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054234 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054234/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054234 Building REAL250005054235 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054235' /scratch/stefan/7922901/working/building/REAL250005054235 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054235 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054235/0 /scratch/stefan/7922901/working/building/REAL250005054235 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/365 `/scratch/stefan/7922901/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@H](O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054235.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054235 none CCC[C@H](O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 146, 115, 146, 146, 115, 115, 70, 47, 17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 438, 115, 70, 70, 47, 47, 17, 17, 17, 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: 1390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054235 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054235 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054235/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054235 Building REAL250005054236 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054236' /scratch/stefan/7922901/working/building/REAL250005054236 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054236 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054236/0 /scratch/stefan/7922901/working/building/REAL250005054236 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/366 `/scratch/stefan/7922901/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(OC)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054236.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054236 none CCC(C)(OC)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 175, 109, 176, 176, 185, 109, 109, 63, 46, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 176, 176, 176, 185, 185, 185, 109, 63, 63, 46, 46, 16, 16, 16, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 923 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054236 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054236 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054236/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054236 Building REAL250005054237 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054237' /scratch/stefan/7922901/working/building/REAL250005054237 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054237 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054237/0 /scratch/stefan/7922901/working/building/REAL250005054237 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/367 `/scratch/stefan/7922901/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054237.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054237 none CC(C)[C@H](O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 170, 201, 118, 170, 170, 118, 118, 57, 44, 21, 10, 21, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 510, 118, 57, 57, 44, 44, 21, 21, 21, 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: 1324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054237 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054237 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054237/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054237 Building REAL250005054238 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054238' /scratch/stefan/7922901/working/building/REAL250005054238 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054238 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054238/0 /scratch/stefan/7922901/working/building/REAL250005054238 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/368 `/scratch/stefan/7922901/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CO)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054238.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054238 none CC(C)C(CO)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [178, 148, 174, 80, 148, 195, 80, 80, 41, 41, 21, 9, 21, 1, 9, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 178, 178, 148, 195, 195, 585, 80, 41, 41, 41, 41, 21, 21, 21, 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: 1606 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054238 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054238 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054238/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054238 Building REAL250005054239 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054239' /scratch/stefan/7922901/working/building/REAL250005054239 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054239 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054239/0 /scratch/stefan/7922901/working/building/REAL250005054239 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/369 `/scratch/stefan/7922901/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054239.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054239 none CCOC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 114, 114, 55, 55, 55, 39, 27, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 114, 114, 55, 39, 39, 27, 27, 13, 13, 13, 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: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054239 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054239 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054239/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054239 Building REAL250005054240 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054240' /scratch/stefan/7922901/working/building/REAL250005054240 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005054240 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054240/0 /scratch/stefan/7922901/working/building/REAL250005054240 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/370 `/scratch/stefan/7922901/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054240.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054240 none CCN1CCC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 117, 113, 113, 113, 76, 58, 23, 10, 23, 1, 10, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 113, 76, 76, 58, 58, 23, 23, 23, 1] 117 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: 454 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: REAL250005054240 none CCN1CCC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 10, 19, 42, 42, 100, 100, 117, 117, 117, 117, 117, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 3, 10, 10, 19, 19, 42, 42, 42, 117] 117 rigid atoms, others: [1, 2, 3, 4, 5, 6, 26, 27, 28, 29, 30] set([0, 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, 38, 39]) total number of confs: 368 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054240 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054240/1 /scratch/stefan/7922901/working/building/REAL250005054240 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/371 `/scratch/stefan/7922901/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+]1CCC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054240.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054240 none CC[N@@H+]1CCC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 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, 7, 7, 1] 9 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: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054240 none CC[N@@H+]1CCC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 8, 8, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 6, 6, 9] 9 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 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, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054240 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `2' /scratch/stefan/7922901/working/building/REAL250005054240/2 /scratch/stefan/7922901/working/building/REAL250005054240 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 2 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/372 `/scratch/stefan/7922901/working/3D/372' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+]1CCC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054240.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005054240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054240/2/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: REAL250005054240 none CC[N@H+]1CCC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 73, 73, 73, 73, 73, 59, 59, 59, 30, 30, 23, 12, 23, 1, 12, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 73, 73, 73, 73, 73, 59, 30, 30, 30, 30, 23, 23, 23, 1] 76 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: 258 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: REAL250005054240 none CC[N@H+]1CCC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 32, 39, 40, 40, 58, 58, 73, 73, 73, 73, 73, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 13, 32, 32, 39, 39, 40, 40, 40, 73] 76 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 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, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 257 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054240 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054240 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054240/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054240/1.* 2: /scratch/stefan/7922901/working/building/REAL250005054240/2.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054240 Building REAL250005054241 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054241' /scratch/stefan/7922901/working/building/REAL250005054241 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054241 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054241/0 /scratch/stefan/7922901/working/building/REAL250005054241 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/373 `/scratch/stefan/7922901/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CCCC1O)C(=O)C1=CC(=O)[N-]O1) `REAL250005054241.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054241 none CN(CCNC(=O)C1CCCC1O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 294 conformations in input total number of sets (complete confs): 294 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 40, 54, 84, 84, 84, 98, 98, 98, 98, 98, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 40, 40, 54, 54, 84, 98, 98, 98, 98, 98, 98, 98, 98, 294, 1] 294 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: 677 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054241 none CN(CCNC(=O)C1CCCC1O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 294 conformations in input total number of sets (complete confs): 294 using faster count positions algorithm for large data unique positions, atoms: [63, 40, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 63, 95, 95, 98, 98, 98, 98, 98, 63, 63, 63, 40, 40, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 98] 294 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38]) total number of confs: 369 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054241 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054241 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054241/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054241 Building REAL250005054242 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054242' /scratch/stefan/7922901/working/building/REAL250005054242 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054242 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054242/0 /scratch/stefan/7922901/working/building/REAL250005054242 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/374 `/scratch/stefan/7922901/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054242.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054242 none C[C@@H](O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 177, 201, 201, 177, 177, 104, 70, 23, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 603, 177, 104, 104, 70, 70, 23, 23, 23, 1] 603 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 1407 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054242 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054242 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054242/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054242 Building REAL250005054243 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054243' /scratch/stefan/7922901/working/building/REAL250005054243 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054243 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054243/0 /scratch/stefan/7922901/working/building/REAL250005054243 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/375 `/scratch/stefan/7922901/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=C(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054243.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054243 none CCC(C)=C(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 132, 132, 132, 90, 132, 90, 90, 51, 40, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 132, 132, 132, 132, 132, 132, 90, 51, 51, 40, 40, 17, 17, 17, 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: 902 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054243 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054243 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054243/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054243 Building REAL250005054244 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054244' /scratch/stefan/7922901/working/building/REAL250005054244 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054244 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054244/0 /scratch/stefan/7922901/working/building/REAL250005054244 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/376 `/scratch/stefan/7922901/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005054244.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054244 none COC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCC1 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.3', '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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 135, 135, 78, 53, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 135, 78, 78, 53, 53, 21, 21, 21, 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: 751 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: REAL250005054244 none COC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCC1 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.3', '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, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 38, 71, 102, 102, 161, 161, 201, 201, 201, 201, 201, 1, 1, 1, 5, 5, 5, 7, 38, 38, 71, 71, 102, 102, 102, 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: 697 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054244 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054244 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054244/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054244 Building REAL250005054245 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054245' /scratch/stefan/7922901/working/building/REAL250005054245 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054245 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054245/0 /scratch/stefan/7922901/working/building/REAL250005054245 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/377 `/scratch/stefan/7922901/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCC(C)(C)O)C(=O)C1=CC(=O)[N-]O1) `REAL250005054245.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054245 none CN(CCNC(=O)CCC(C)(C)O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 6, 13, 23, 27, 47, 47, 47, 141, 141, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 23, 23, 27, 27, 47, 141, 141, 141, 141, 201, 201, 201, 201, 201, 201, 603, 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: 1507 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054245 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054245 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054245/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054245 Building REAL250005054246 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054246' /scratch/stefan/7922901/working/building/REAL250005054246 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054246 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054246/0 /scratch/stefan/7922901/working/building/REAL250005054246 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/378 `/scratch/stefan/7922901/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CSN=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054246.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054246 none CN(CCNC(=O)C1=CSN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 14, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 42, 50, 68, 68, 68, 98, 98, 98, 98, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21, 42, 42, 50, 50, 68, 98, 98, 1] 98 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: 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: REAL250005054246 none CN(CCNC(=O)C1=CSN=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 14, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [57, 39, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 57, 94, 94, 98, 98, 98, 98, 98, 57, 57, 57, 39, 39, 25, 25, 5, 1, 1, 98] 98 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054246 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054246 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054246/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054246 Building REAL250005054247 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054247' /scratch/stefan/7922901/working/building/REAL250005054247 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054247 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054247/0 /scratch/stefan/7922901/working/building/REAL250005054247 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/379 `/scratch/stefan/7922901/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C)(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054247.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054247 none CC1CC(C)(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 86, 201, 86, 86, 62, 52, 18, 8, 18, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 86, 62, 62, 52, 52, 18, 18, 18, 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: 662 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054247 none CC1CC(C)(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 32, 57, 95, 95, 179, 179, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 7, 32, 32, 57, 57, 95, 95, 95, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 40, 20, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 728 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054247 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054247 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054247/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054247 Building REAL250005054248 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054248' /scratch/stefan/7922901/working/building/REAL250005054248 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054248 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054248/0 /scratch/stefan/7922901/working/building/REAL250005054248 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/380 `/scratch/stefan/7922901/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054248.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054248 none CNC(=O)CCC(=O)NCCN(C)C(=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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 201, 193, 126, 126, 126, 78, 46, 17, 8, 17, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 199, 199, 193, 193, 126, 78, 78, 46, 46, 17, 17, 17, 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: 881 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054248 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054248 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054248/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054248 Building REAL250005054249 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054249' /scratch/stefan/7922901/working/building/REAL250005054249 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054249 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054249/0 /scratch/stefan/7922901/working/building/REAL250005054249 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/381 `/scratch/stefan/7922901/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCCCF)C(=O)C1=CC(=O)[N-]O1) `REAL250005054249.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054249 none CN(CCNC(=O)CCCCF)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 21, 21, 45, 45, 45, 137, 167, 199, 199, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 21, 21, 21, 21, 45, 137, 137, 181, 181, 198, 198, 201, 201, 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: 930 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054249 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054249 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054249/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054249 Building REAL250005054250 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054250' /scratch/stefan/7922901/working/building/REAL250005054250 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054250 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054250/0 /scratch/stefan/7922901/working/building/REAL250005054250 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/382 `/scratch/stefan/7922901/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C=CCO)C(=O)C1=CC(=O)[N-]O1) `REAL250005054250.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054250 none CN(CCNC(=O)C=CCO)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 12, 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, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 6, 17, 39, 50, 86, 86, 86, 169, 169, 201, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 39, 39, 50, 50, 86, 169, 169, 201, 201, 603, 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: 1399 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054250 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054250 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054250/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054250 Building REAL250005054251 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054251' /scratch/stefan/7922901/working/building/REAL250005054251 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054251 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054251/0 /scratch/stefan/7922901/working/building/REAL250005054251 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/383 `/scratch/stefan/7922901/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1=CN=CO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054251.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054251 none CN(CCNC(=O)CC1=CN=CO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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, 6, 17, 25, 25, 47, 47, 47, 142, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 25, 25, 25, 25, 47, 142, 142, 201, 201, 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: 626 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054251 none CN(CCNC(=O)CC1=CN=CO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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: [183, 158, 120, 31, 31, 5, 31, 1, 1, 1, 1, 1, 1, 183, 201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 158, 158, 120, 120, 31, 5, 5, 1, 1, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 833 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054251 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054251 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054251/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054251 Building REAL250005054252 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054252' /scratch/stefan/7922901/working/building/REAL250005054252 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054252 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054252/0 /scratch/stefan/7922901/working/building/REAL250005054252 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/384 `/scratch/stefan/7922901/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054252.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054252 none COC(C)(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 134, 201, 201, 134, 134, 65, 47, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 134, 65, 65, 47, 47, 15, 15, 15, 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: 826 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054252 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054252 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054252/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054252 Building REAL250005054253 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054253' /scratch/stefan/7922901/working/building/REAL250005054253 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054253 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054253/0 /scratch/stefan/7922901/working/building/REAL250005054253 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/385 `/scratch/stefan/7922901/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(C)(C)[NH+](C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054253.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054253 none CN(CCNC(=O)C(C)(C)[NH+](C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 9, 9, 9, 13, 13, 13, 13, 13, 13, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1] 13 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: 47 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054253 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054253 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054253/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054253 Building REAL250005054254 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054254' /scratch/stefan/7922901/working/building/REAL250005054254 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054254 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054254/0 /scratch/stefan/7922901/working/building/REAL250005054254 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/386 `/scratch/stefan/7922901/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(F)(F)CO)C(=O)C1=CC(=O)[N-]O1) `REAL250005054254.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054254 none CN(CCNC(=O)C(F)(F)CO)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 15, 15, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 9, 9, 15, 15, 15, 35, 35, 35, 37, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 15, 37, 37, 111, 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: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054254 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054254 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054254/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054254 Building REAL250005054255 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054255' /scratch/stefan/7922901/working/building/REAL250005054255 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054255 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054255/0 /scratch/stefan/7922901/working/building/REAL250005054255 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/387 `/scratch/stefan/7922901/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCCCO)C(=O)C1=CC(=O)[N-]O1) `REAL250005054255.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054255 none CN(CCNC(=O)CCCCO)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 15, 25, 27, 36, 36, 36, 127, 165, 193, 199, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 25, 25, 27, 27, 36, 127, 127, 182, 182, 193, 193, 201, 201, 597, 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: 1594 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054255 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054255 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054255/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054255 Building REAL250005054256 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054256' /scratch/stefan/7922901/working/building/REAL250005054256 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054256 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054256/0 /scratch/stefan/7922901/working/building/REAL250005054256 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/388 `/scratch/stefan/7922901/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)C=NO1) `REAL250005054256.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054256 none CC1=C(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 201, 137, 137, 137, 81, 59, 22, 9, 22, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 137, 81, 81, 59, 59, 22, 22, 22, 1, 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]) total number of confs: 609 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: REAL250005054256 none CC1=C(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 9, 9, 9, 43, 77, 125, 125, 186, 186, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 9, 43, 43, 77, 77, 126, 126, 126, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 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: 753 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054256 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054256 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054256/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054256 Building REAL250005054257 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054257' /scratch/stefan/7922901/working/building/REAL250005054257 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054257 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054257/0 /scratch/stefan/7922901/working/building/REAL250005054257 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/389 `/scratch/stefan/7922901/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CNC(=O)C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054257.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054257 none CN(CCNC(=O)C1CNC(=O)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 20, 37, 41, 63, 63, 63, 109, 109, 109, 109, 109, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 37, 37, 41, 41, 63, 109, 109, 109, 109, 109, 109, 1] 109 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: 379 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054257 none CN(CCNC(=O)C1CNC(=O)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [83, 68, 45, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 83, 107, 107, 109, 109, 109, 109, 109, 83, 83, 83, 68, 68, 45, 45, 9, 1, 1, 1, 1, 1, 1, 109] 109 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054257 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054257 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054257/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054257 Building REAL250005054258 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054258' /scratch/stefan/7922901/working/building/REAL250005054258 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054258 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054258/0 /scratch/stefan/7922901/working/building/REAL250005054258 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/390 `/scratch/stefan/7922901/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1CNC(=O)N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054258.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054258 none CN(CCNC(=O)[C@@H]1CNC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.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, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 26, 26, 38, 38, 38, 63, 63, 63, 63, 63, 63, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 26, 26, 26, 26, 38, 63, 63, 63, 63, 1] 63 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054258 none CN(CCNC(=O)[C@@H]1CNC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.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, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [53, 48, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 53, 61, 61, 63, 63, 63, 63, 63, 53, 53, 53, 48, 48, 36, 36, 10, 1, 1, 1, 1, 63] 63 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054258 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054258 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054258/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054258 Building REAL250005054259 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054259' /scratch/stefan/7922901/working/building/REAL250005054259 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054259 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054259/0 /scratch/stefan/7922901/working/building/REAL250005054259 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/391 `/scratch/stefan/7922901/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CN=CS1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054259.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054259 none CN(CCNC(=O)C1=CN=CS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 10, 26, 53, 67, 101, 101, 101, 165, 165, 165, 165, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 26, 53, 53, 67, 67, 101, 165, 165, 1] 165 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: 505 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054259 none CN(CCNC(=O)C1=CN=CS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [97, 63, 41, 10, 10, 1, 10, 1, 1, 1, 1, 1, 97, 157, 157, 165, 165, 165, 165, 165, 97, 97, 97, 63, 63, 40, 40, 10, 1, 1, 165] 165 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054259 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054259 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054259/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054259 Building REAL250005054260 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054260' /scratch/stefan/7922901/working/building/REAL250005054260 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054260 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054260/0 /scratch/stefan/7922901/working/building/REAL250005054260 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/392 `/scratch/stefan/7922901/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)N1) `REAL250005054260.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054260 none CC1=CC=C(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 185, 185, 185, 115, 91, 36, 12, 36, 1, 12, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 185, 115, 115, 91, 91, 36, 36, 36, 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: 709 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: REAL250005054260 none CC1=CC=C(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 6, 6, 6, 35, 61, 99, 99, 167, 167, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 6, 34, 34, 61, 61, 99, 99, 99, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 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: 668 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054260 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054260 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054260/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054260 Building REAL250005054261 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054261' /scratch/stefan/7922901/working/building/REAL250005054261 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054261 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054261/0 /scratch/stefan/7922901/working/building/REAL250005054261 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/393 `/scratch/stefan/7922901/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(CO)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054261.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054261 none CN(CCNC(=O)C1(CO)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 40, 47, 88, 88, 88, 186, 201, 186, 186, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 40, 40, 47, 47, 88, 201, 201, 603, 186, 186, 186, 186, 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: 1303 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: REAL250005054261 none CN(CCNC(=O)C1(CO)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [108, 65, 36, 7, 7, 1, 7, 1, 1, 9, 1, 1, 108, 170, 170, 186, 186, 186, 186, 186, 108, 108, 108, 65, 65, 36, 36, 7, 9, 9, 27, 1, 1, 1, 1, 186] 603 rigid atoms, others: [32, 33, 34, 5, 7, 8, 10, 11, 31] set([0, 1, 2, 3, 4, 6, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 720 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054261 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054261 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054261/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054261 Building REAL250005054262 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054262' /scratch/stefan/7922901/working/building/REAL250005054262 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054262 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054262/0 /scratch/stefan/7922901/working/building/REAL250005054262 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/394 `/scratch/stefan/7922901/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(CC(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054262.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054262 none COC1(CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 47, 47, 47, 34, 30, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 47, 34, 34, 30, 30, 15, 15, 15, 1, 53, 53, 53, 53] 53 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: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054262 none COC1(CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 4, 10, 10, 10, 30, 36, 45, 45, 52, 52, 53, 53, 53, 53, 53, 1, 1, 3, 3, 3, 4, 4, 10, 30, 30, 36, 36, 45, 45, 45, 53, 1, 1, 1, 1] 53 rigid atoms, others: [1, 2, 3, 36, 37, 35, 19, 20, 38] set([0, 4, 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: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054262 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054262 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054262/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054262 Building REAL250005054263 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054263' /scratch/stefan/7922901/working/building/REAL250005054263 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054263 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054263/0 /scratch/stefan/7922901/working/building/REAL250005054263 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/395 `/scratch/stefan/7922901/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054263.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054263 none CC[C@H](C)[C@H](O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 179, 200, 200, 131, 179, 179, 131, 131, 71, 50, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 200, 537, 131, 71, 71, 50, 50, 19, 19, 19, 1] 603 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: 1415 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054263 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054263 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054263/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054263 Building REAL250005054264 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054264' /scratch/stefan/7922901/working/building/REAL250005054264 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054264 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054264/0 /scratch/stefan/7922901/working/building/REAL250005054264 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/396 `/scratch/stefan/7922901/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]12C[C@H]1[C@H](O)C2)C(=O)C1=CC(=O)[N-]O1) `REAL250005054264.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054264 none CN(CCNC(=O)[C@]12C[C@H]1[C@H](O)C2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 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: [21, 8, 21, 48, 59, 90, 90, 90, 201, 201, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 48, 48, 59, 59, 90, 201, 201, 603, 201, 201, 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: 1101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054264 none CN(CCNC(=O)[C@]12C[C@H]1[C@H](O)C2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 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: [116, 70, 38, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 116, 190, 190, 201, 201, 201, 201, 201, 116, 116, 116, 70, 70, 38, 38, 7, 1, 1, 6, 1, 1, 201] 603 rigid atoms, others: [32, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36]) total number of confs: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054264 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054264 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054264/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054264 Building REAL250005054265 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054265' /scratch/stefan/7922901/working/building/REAL250005054265 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054265 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054265/0 /scratch/stefan/7922901/working/building/REAL250005054265 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/397 `/scratch/stefan/7922901/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054265.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054265 none COC(F)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 116, 195, 116, 116, 69, 48, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 116, 69, 69, 48, 48, 19, 19, 19, 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: 799 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054265 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054265 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054265/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054265 Building REAL250005054266 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054266' /scratch/stefan/7922901/working/building/REAL250005054266 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054266 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054266/0 /scratch/stefan/7922901/working/building/REAL250005054266 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/398 `/scratch/stefan/7922901/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C12CC1CC2)C(=O)C1=CC(=O)[N-]O1) `REAL250005054266.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054266 none CN(CCNC(=O)C12CC1CC2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 22, 46, 56, 70, 70, 70, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 46, 46, 56, 56, 70, 201, 201, 201, 201, 201, 201, 201, 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: 444 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: REAL250005054266 none CN(CCNC(=O)C12CC1CC2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 65, 36, 7, 7, 1, 7, 1, 1, 1, 1, 1, 112, 192, 192, 201, 201, 201, 201, 201, 112, 112, 112, 65, 65, 36, 36, 7, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35]) total number of confs: 746 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054266 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054266 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054266/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054266 Building REAL250005054267 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054267' /scratch/stefan/7922901/working/building/REAL250005054267 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054267 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054267/0 /scratch/stefan/7922901/working/building/REAL250005054267 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/399 `/scratch/stefan/7922901/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054267.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054267 none CCCC(C)=CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 108, 108, 108, 52, 52, 52, 29, 25, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 199, 108, 108, 108, 108, 52, 29, 29, 25, 25, 14, 14, 14, 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.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054267 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054267 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054267/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054267 Building REAL250005054268 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054268' /scratch/stefan/7922901/working/building/REAL250005054268 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054268 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054268/0 /scratch/stefan/7922901/working/building/REAL250005054268 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/400 `/scratch/stefan/7922901/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054268.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054268 none C=C[C@H](C)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 144, 173, 173, 72, 72, 72, 59, 43, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 173, 173, 144, 144, 72, 59, 59, 43, 43, 16, 16, 16, 1] 173 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: 806 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054268 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054268 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054268/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054268 Building REAL250005054269 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054269' /scratch/stefan/7922901/working/building/REAL250005054269 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054269 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054269/0 /scratch/stefan/7922901/working/building/REAL250005054269 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/401 `/scratch/stefan/7922901/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C=CC1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054269.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054269 none CN(CCNC(=O)C=CC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 15, 31, 37, 63, 63, 63, 142, 142, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 31, 31, 37, 37, 63, 142, 142, 201, 201, 201, 201, 201, 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: 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: REAL250005054269 none CN(CCNC(=O)C=CC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 127, 92, 33, 33, 10, 32, 10, 1, 1, 1, 1, 153, 196, 196, 201, 201, 201, 201, 201, 153, 153, 153, 127, 127, 92, 92, 33, 10, 10, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 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, 28, 29, 35]) total number of confs: 806 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054269 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054269 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054269/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054269 Building REAL250005054270 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054270' /scratch/stefan/7922901/working/building/REAL250005054270 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054270 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054270/0 /scratch/stefan/7922901/working/building/REAL250005054270 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/402 `/scratch/stefan/7922901/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054270.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054270 none CC=C(CC)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 73, 151, 201, 73, 73, 53, 47, 17, 8, 17, 1, 8, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 201, 201, 201, 201, 201, 73, 53, 53, 47, 47, 17, 17, 17, 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: 815 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054270 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054270 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054270/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054270 Building REAL250005054271 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054271' /scratch/stefan/7922901/working/building/REAL250005054271 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054271 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054271/0 /scratch/stefan/7922901/working/building/REAL250005054271 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/403 `/scratch/stefan/7922901/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC12CC(C1)C2)C(=O)C1=CC(=O)[N-]O1) `REAL250005054271.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054271 none CN(CCNC(=O)CC12CC(C1)C2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 44, 52, 81, 81, 81, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 44, 44, 52, 52, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 831 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054271 none CN(CCNC(=O)CC12CC(C1)C2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 127, 98, 35, 35, 7, 35, 1, 1, 1, 1, 1, 1, 160, 198, 198, 201, 201, 201, 201, 201, 160, 160, 160, 127, 127, 98, 98, 35, 7, 7, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38]) total number of confs: 803 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054271 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054271 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054271/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054271 Building REAL250005054272 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054272' /scratch/stefan/7922901/working/building/REAL250005054272 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054272 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054272/0 /scratch/stefan/7922901/working/building/REAL250005054272 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/404 `/scratch/stefan/7922901/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C(C)O) `REAL250005054272.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054272 none CCC(C(=O)NCCN(C)C(=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.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7, 7] 1 hydrogens need rotated 597 conformations in input total number of sets (complete confs): 597 using faster count positions algorithm for large data unique positions, atoms: [166, 147, 91, 91, 91, 49, 46, 24, 11, 24, 1, 11, 1, 1, 1, 1, 1, 1, 147, 191, 192, 168, 168, 168, 168, 168, 147, 91, 49, 49, 46, 46, 24, 24, 24, 1, 192, 192, 192, 192, 576] 597 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: 1536 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054272 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054272 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054272/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054272 Building REAL250005054273 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054273' /scratch/stefan/7922901/working/building/REAL250005054273 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054273 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054273/0 /scratch/stefan/7922901/working/building/REAL250005054273 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/405 `/scratch/stefan/7922901/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054273.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054273 none C=CC(C)(O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 201, 201, 119, 119, 72, 52, 23, 10, 23, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 119, 72, 72, 52, 52, 23, 23, 23, 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: 1419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054273 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054273 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054273/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054273 Building REAL250005054274 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054274' /scratch/stefan/7922901/working/building/REAL250005054274 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054274 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054274/0 /scratch/stefan/7922901/working/building/REAL250005054274 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/406 `/scratch/stefan/7922901/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CO)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054274.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054274 none CCC(C)(CO)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 351 conformations in input total number of sets (complete confs): 351 using faster count positions algorithm for large data unique positions, atoms: [102, 85, 55, 85, 85, 117, 55, 55, 34, 34, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 85, 85, 85, 117, 117, 351, 55, 34, 34, 34, 34, 21, 21, 21, 1] 351 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: 979 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054274 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054274 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054274/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054274 Building REAL250005054275 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054275' /scratch/stefan/7922901/working/building/REAL250005054275 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054275 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054275/0 /scratch/stefan/7922901/working/building/REAL250005054275 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/407 `/scratch/stefan/7922901/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1([NH+](C)C)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054275.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054275 none CN(CCNC(=O)C1([NH+](C)C)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 17, 17, 24, 24, 24, 26, 26, 26, 26, 26, 26, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 17, 17, 17, 17, 24, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1] 26 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: 95 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054275 none CN(CCNC(=O)C1([NH+](C)C)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 13, 5, 5, 1, 5, 1, 1, 4, 4, 4, 1, 1, 22, 24, 24, 26, 26, 26, 26, 26, 22, 22, 22, 15, 15, 13, 13, 5, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 26] 26 rigid atoms, others: [36, 5, 38, 7, 8, 39, 12, 13, 37] set([0, 1, 2, 3, 4, 6, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054275 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054275/1 /scratch/stefan/7922901/working/building/REAL250005054275 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/408 `/scratch/stefan/7922901/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054275.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054275 none CN(C)C1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 10, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 28, 28, 28, 28, 24, 14, 10, 14, 1, 10, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 28, 28, 28, 24, 24, 14, 14, 14, 1, 38, 38, 38, 38] 38 rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 149 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: REAL250005054275 none CN(C)C1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 10, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 3, 3, 3, 9, 10, 15, 15, 19, 19, 38, 38, 38, 38, 38, 1, 1, 3, 3, 3, 3, 3, 3, 3, 9, 9, 10, 10, 15, 15, 15, 38, 1, 1, 1, 1] 38 rigid atoms, others: [1, 3, 4, 37, 38, 39, 19, 20, 36] set([0, 2, 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, 35]) total number of confs: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054275 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054275 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054275/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054275/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054275 Building REAL250005054276 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054276' /scratch/stefan/7922901/working/building/REAL250005054276 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054276 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054276/0 /scratch/stefan/7922901/working/building/REAL250005054276 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/409 `/scratch/stefan/7922901/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C12CC(C1)CO2)C(=O)C1=CC(=O)[N-]O1) `REAL250005054276.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054276 none CN(CCNC(=O)C12CC(C1)CO2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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: [18, 6, 18, 28, 28, 54, 54, 54, 122, 122, 122, 122, 122, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 28, 28, 28, 28, 54, 122, 122, 122, 122, 122, 122, 122, 1] 122 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: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054276 none CN(CCNC(=O)C12CC(C1)CO2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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: [97, 81, 60, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 97, 121, 121, 122, 122, 122, 122, 122, 97, 97, 97, 81, 81, 60, 60, 13, 1, 1, 1, 1, 1, 1, 1, 122] 122 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054276 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054276 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054276/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054276 Building REAL250005054277 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054277' /scratch/stefan/7922901/working/building/REAL250005054277 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054277 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054277/0 /scratch/stefan/7922901/working/building/REAL250005054277 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/410 `/scratch/stefan/7922901/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C(C)(C)O) `REAL250005054277.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054277 none C[C@@H](C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 312 conformations in input total number of sets (complete confs): 312 using faster count positions algorithm for large data unique positions, atoms: [94, 74, 94, 74, 74, 41, 38, 22, 8, 22, 1, 8, 1, 1, 1, 1, 1, 1, 94, 104, 100, 104, 94, 94, 94, 74, 41, 41, 38, 38, 22, 22, 22, 1, 104, 104, 104, 104, 104, 104, 312] 312 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: 747 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054277 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054277 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054277/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054277 Building REAL250005054278 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054278' /scratch/stefan/7922901/working/building/REAL250005054278 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054278 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054278/0 /scratch/stefan/7922901/working/building/REAL250005054278 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/411 `/scratch/stefan/7922901/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C12CC(C1)OC2)C(=O)C1=CC(=O)[N-]O1) `REAL250005054278.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054278 none CN(CCNC(=O)C12CC(C1)OC2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 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: [21, 8, 21, 39, 45, 52, 52, 52, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 39, 39, 45, 45, 52, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005054278 none CN(CCNC(=O)C12CC(C1)OC2)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 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: [112, 66, 36, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 112, 195, 195, 201, 201, 201, 201, 201, 112, 112, 112, 66, 66, 36, 36, 7, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 754 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054278 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054278 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054278/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054278 Building REAL250005054279 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054279' /scratch/stefan/7922901/working/building/REAL250005054279 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054279 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054279/0 /scratch/stefan/7922901/working/building/REAL250005054279 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/412 `/scratch/stefan/7922901/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C1CC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054279.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054279 none CC(O)C1CC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 167, 167, 167, 113, 86, 33, 12, 33, 1, 12, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 201, 201, 201, 201, 167, 113, 113, 86, 86, 33, 33, 33, 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: 1378 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054279 none CC(O)C1CC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 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, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 2, 1, 1, 1, 1, 7, 7, 7, 33, 55, 88, 88, 151, 151, 201, 201, 201, 201, 201, 2, 2, 2, 2, 6, 1, 1, 1, 1, 7, 33, 33, 55, 55, 88, 88, 88, 201] 603 rigid atoms, others: [1, 3, 4, 5, 6, 26, 27, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 673 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054279 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054279 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054279/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054279 Building REAL250005054280 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054280' /scratch/stefan/7922901/working/building/REAL250005054280 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054280 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054280/0 /scratch/stefan/7922901/working/building/REAL250005054280 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/413 `/scratch/stefan/7922901/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@]2(C(=O)NCCN(C)C(=O)C3=CC(=O)[N-]O3)C[C@@H]12) `REAL250005054280.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054280 none C[C@@H]1C[C@@]2(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 77, 77, 77, 55, 45, 18, 8, 18, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 77, 55, 55, 45, 45, 18, 18, 18, 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: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054280 none C[C@@H]1C[C@@]2(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 33, 57, 97, 97, 183, 183, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 7, 33, 33, 57, 57, 97, 97, 97, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 26, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054280 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054280 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054280/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054280 Building REAL250005054281 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054281' /scratch/stefan/7922901/working/building/REAL250005054281 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054281 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054281/0 /scratch/stefan/7922901/working/building/REAL250005054281 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/414 `/scratch/stefan/7922901/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CN1C=NC=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054281.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054281 none CN(CCNC(=O)CN1C=NC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 27, 27, 56, 56, 56, 160, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 56, 160, 160, 201, 201, 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: REAL250005054281 none CN(CCNC(=O)CN1C=NC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 8, 1, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 153, 121, 42, 42, 8, 42, 1, 1, 1, 1, 1, 1, 172, 198, 198, 201, 201, 201, 201, 201, 172, 172, 172, 153, 153, 121, 121, 42, 8, 8, 1, 1, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 806 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054281 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054281 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054281/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054281 Building REAL250005054282 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054282' /scratch/stefan/7922901/working/building/REAL250005054282 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054282 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054282/0 /scratch/stefan/7922901/working/building/REAL250005054282 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/415 `/scratch/stefan/7922901/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C#CC1(C)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054282.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054282 none CN(CCNC(=O)C#CC1(C)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 10, 29, 65, 89, 131, 131, 131, 131, 131, 131, 131, 131, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 65, 65, 89, 89, 131, 131, 131, 131, 131, 131, 131, 131, 1] 131 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: 515 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: REAL250005054282 none CN(CCNC(=O)C#CC1(C)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [47, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 109, 109, 131, 131, 131, 131, 131, 47, 47, 47, 21, 21, 9, 9, 1, 2, 2, 2, 1, 1, 1, 1, 131] 131 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 28] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 36]) total number of confs: 399 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054282 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054282 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054282/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054282 Building REAL250005054283 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054283' /scratch/stefan/7922901/working/building/REAL250005054283 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054283 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054283/0 /scratch/stefan/7922901/working/building/REAL250005054283 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/416 `/scratch/stefan/7922901/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054283.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054283 none CN(CCNC(=O)C1=CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [28, 10, 28, 56, 76, 109, 109, 109, 109, 109, 109, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 56, 56, 76, 76, 109, 109, 109, 109, 109, 109, 1] 109 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: 410 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054283 none CN(CCNC(=O)C1=CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [57, 31, 18, 6, 6, 1, 6, 1, 1, 1, 1, 57, 99, 99, 109, 109, 109, 109, 109, 57, 57, 57, 31, 31, 18, 18, 6, 1, 1, 1, 1, 1, 109] 109 rigid atoms, others: [5, 7, 8, 9, 10, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054283 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054283 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054283/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054283 Building REAL250005054284 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054284' /scratch/stefan/7922901/working/building/REAL250005054284 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054284 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054284/0 /scratch/stefan/7922901/working/building/REAL250005054284 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/417 `/scratch/stefan/7922901/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC=C(F)O1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054284.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054284 none CN(CCNC(=O)C1=CC=C(F)O1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 20, 39, 43, 71, 71, 71, 106, 106, 106, 106, 106, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 39, 39, 43, 43, 71, 106, 106, 1] 106 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: 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: REAL250005054284 none CN(CCNC(=O)C1=CC=C(F)O1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [68, 48, 36, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 68, 106, 106, 106, 106, 106, 106, 106, 68, 68, 68, 48, 48, 36, 36, 9, 1, 1, 106] 106 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054284 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054284 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054284/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054284 Building REAL250005054285 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054285' /scratch/stefan/7922901/working/building/REAL250005054285 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054285 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054285/0 /scratch/stefan/7922901/working/building/REAL250005054285 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/418 `/scratch/stefan/7922901/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054285.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054285 none CON=CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 171, 171, 171, 99, 67, 29, 10, 29, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 171, 99, 99, 67, 67, 29, 29, 29, 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: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054285 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054285 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054285/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054285 Building REAL250005054286 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054286' /scratch/stefan/7922901/working/building/REAL250005054286 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054286 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054286/0 /scratch/stefan/7922901/working/building/REAL250005054286 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/419 `/scratch/stefan/7922901/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054286.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054286 none C#CCC(C)(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 130, 80, 130, 130, 80, 80, 57, 47, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 166, 166, 166, 130, 130, 130, 130, 130, 130, 80, 57, 57, 47, 47, 16, 16, 16, 1] 166 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: 765 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054286 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054286 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054286/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054286 Building REAL250005054287 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054287' /scratch/stefan/7922901/working/building/REAL250005054287 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054287 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054287/0 /scratch/stefan/7922901/working/building/REAL250005054287 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/420 `/scratch/stefan/7922901/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C(N)=O) `REAL250005054287.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054287 none CN(CC(=O)NCCN(C)C(=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.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 88, 55, 55, 55, 47, 31, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 98, 88, 88, 55, 47, 47, 31, 31, 16, 16, 16, 1, 98, 98] 98 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]) total number of confs: 433 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054287 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054287 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054287/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054287 Building REAL250005054288 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054288' /scratch/stefan/7922901/working/building/REAL250005054288 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054288 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054288/0 /scratch/stefan/7922901/working/building/REAL250005054288 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/421 `/scratch/stefan/7922901/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NC(=O)N[N-]1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054288.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054288 none CN(CCNC(=O)C1=NC(=O)N[N-]1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 5, 5, 8, 1, 11, 1, 8, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 19, 19, 26, 26, 26, 49, 49, 49, 49, 49, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 19, 19, 19, 19, 26, 49, 1] 49 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054288 none CN(CCNC(=O)C1=NC(=O)N[N-]1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 5, 5, 8, 1, 11, 1, 8, 1, 11, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 44, 49, 49, 49, 49, 49, 49, 49, 44, 44, 44, 44, 44, 36, 36, 12, 1, 49] 49 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054288 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054288 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054288/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054288 Building REAL250005054289 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054289' /scratch/stefan/7922901/working/building/REAL250005054289 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054289 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054289/0 /scratch/stefan/7922901/working/building/REAL250005054289 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/422 `/scratch/stefan/7922901/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(F)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054289.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054289 none CN(CCNC(=O)C1(F)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 20, 32, 34, 65, 65, 65, 134, 134, 134, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 32, 32, 34, 34, 65, 134, 134, 134, 134, 1] 134 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: 428 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: REAL250005054289 none CN(CCNC(=O)C1(F)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [107, 82, 58, 13, 13, 1, 13, 1, 1, 1, 1, 107, 130, 130, 134, 134, 134, 134, 134, 107, 107, 107, 82, 82, 58, 58, 13, 1, 1, 1, 1, 134] 134 rigid atoms, others: [5, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 538 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054289 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054289 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054289/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054289 Building REAL250005054290 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054290' /scratch/stefan/7922901/working/building/REAL250005054290 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054290 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054290/0 /scratch/stefan/7922901/working/building/REAL250005054290 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/423 `/scratch/stefan/7922901/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)COCCO)C(=O)C1=CC(=O)[N-]O1) `REAL250005054290.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054290 none CN(CCNC(=O)COCCO)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 29, 37, 45, 45, 45, 100, 165, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 29, 29, 37, 37, 45, 100, 100, 201, 201, 201, 201, 603, 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: 1338 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054290 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054290 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054290/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054290 Building REAL250005054291 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054291' /scratch/stefan/7922901/working/building/REAL250005054291 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054291 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054291/0 /scratch/stefan/7922901/working/building/REAL250005054291 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/424 `/scratch/stefan/7922901/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(C)(C)CF)C(=O)C1=CC(=O)[N-]O1) `REAL250005054291.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054291 none CN(CCNC(=O)C(C)(C)CF)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 40, 52, 97, 97, 97, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 40, 40, 52, 52, 97, 201, 201, 201, 201, 201, 201, 201, 201, 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: 815 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054291 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054291 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054291/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054291 Building REAL250005054292 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054292' /scratch/stefan/7922901/working/building/REAL250005054292 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054292 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054292/0 /scratch/stefan/7922901/working/building/REAL250005054292 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/425 `/scratch/stefan/7922901/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054292.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054292 none CC(C)[C@@H](O)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 339 conformations in input total number of sets (complete confs): 339 using faster count positions algorithm for large data unique positions, atoms: [113, 104, 113, 102, 104, 104, 65, 65, 65, 53, 37, 17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 113, 113, 312, 102, 102, 65, 53, 53, 37, 37, 17, 17, 17, 1] 339 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: 811 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054292 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054292 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054292/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054292 Building REAL250005054293 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054293' /scratch/stefan/7922901/working/building/REAL250005054293 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054293 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054293/0 /scratch/stefan/7922901/working/building/REAL250005054293 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/426 `/scratch/stefan/7922901/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054293.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054293 none CSC1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 14, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 176, 105, 105, 105, 66, 52, 21, 10, 21, 1, 10, 1, 1, 1, 1, 1, 1, 176, 176, 201, 201, 201, 105, 66, 66, 52, 52, 21, 21, 21, 1, 176, 176, 176, 176] 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: 665 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054293 none CSC1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 14, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 45, 75, 107, 107, 150, 150, 176, 176, 176, 176, 176, 1, 1, 7, 7, 7, 10, 45, 45, 75, 75, 107, 107, 107, 176, 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: 657 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054293 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054293 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054293/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054293 Building REAL250005054294 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054294' /scratch/stefan/7922901/working/building/REAL250005054294 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054294 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054294/0 /scratch/stefan/7922901/working/building/REAL250005054294 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/427 `/scratch/stefan/7922901/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NOCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054294.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054294 none CN(CCNC(=O)C1=NOCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 17, 24, 24, 39, 39, 39, 45, 45, 45, 45, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 24, 24, 24, 24, 39, 45, 45, 45, 45, 1] 45 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: 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: REAL250005054294 none CN(CCNC(=O)C1=NOCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [41, 37, 32, 12, 12, 1, 12, 1, 1, 1, 1, 1, 41, 45, 45, 45, 45, 45, 45, 45, 41, 41, 41, 37, 37, 32, 32, 12, 1, 1, 1, 1, 45] 45 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054294 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054294 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054294/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054294 Building REAL250005054295 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054295' /scratch/stefan/7922901/working/building/REAL250005054295 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054295 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054295/0 /scratch/stefan/7922901/working/building/REAL250005054295 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/428 `/scratch/stefan/7922901/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(CCO)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054295.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054295 none CN(CCNC(=O)C1(CCO)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 8, 22, 49, 51, 97, 97, 97, 158, 201, 201, 158, 158, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 49, 49, 51, 51, 97, 201, 201, 201, 201, 603, 158, 158, 158, 158, 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: 1386 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054295 none CN(CCNC(=O)C1(CCO)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [78, 50, 30, 7, 7, 1, 7, 1, 1, 7, 13, 1, 1, 78, 132, 132, 158, 158, 158, 158, 158, 78, 78, 78, 50, 50, 30, 30, 7, 7, 7, 13, 13, 39, 1, 1, 1, 1, 158] 603 rigid atoms, others: [34, 35, 36, 5, 7, 8, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 9, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 622 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054295 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054295 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054295/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054295 Building REAL250005054296 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054296' /scratch/stefan/7922901/working/building/REAL250005054296 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054296 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054296/0 /scratch/stefan/7922901/working/building/REAL250005054296 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/429 `/scratch/stefan/7922901/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054296.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054296 none CC(C)C(C)(O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [197, 193, 201, 135, 193, 193, 135, 135, 79, 48, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 579, 135, 79, 79, 48, 48, 20, 20, 20, 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: 1462 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054296 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054296 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054296/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054296 Building REAL250005054297 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054297' /scratch/stefan/7922901/working/building/REAL250005054297 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054297 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054297/0 /scratch/stefan/7922901/working/building/REAL250005054297 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/430 `/scratch/stefan/7922901/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C[NH+](C)C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054297.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054297 none CC(C[NH+](C)C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 6, 9, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 1] 15 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: 56 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054297 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054297 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054297/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054297 Building REAL250005054298 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054298' /scratch/stefan/7922901/working/building/REAL250005054298 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054298 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054298/0 /scratch/stefan/7922901/working/building/REAL250005054298 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/431 `/scratch/stefan/7922901/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NN=CS1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054298.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054298 none CN(CCNC(=O)C1=NN=CS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 21, 21, 33, 33, 33, 45, 45, 45, 45, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 21, 21, 21, 21, 33, 45, 1] 45 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: 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: REAL250005054298 none CN(CCNC(=O)C1=NN=CS1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 14, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [31, 29, 21, 11, 11, 1, 11, 1, 1, 1, 1, 1, 31, 45, 45, 45, 45, 45, 45, 45, 31, 31, 31, 29, 29, 21, 21, 11, 1, 45] 45 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054298 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054298 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054298/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054298 Building REAL250005054299 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054299' /scratch/stefan/7922901/working/building/REAL250005054299 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054299 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054299/0 /scratch/stefan/7922901/working/building/REAL250005054299 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/432 `/scratch/stefan/7922901/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(F)C1CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054299.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054299 none CN(CCNC(=O)C(F)C1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 8, 20, 27, 27, 52, 52, 52, 100, 100, 129, 129, 129, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 52, 100, 129, 129, 129, 129, 129, 129, 129, 1] 129 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: 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: REAL250005054299 none CN(CCNC(=O)C(F)C1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [118, 112, 92, 37, 37, 8, 37, 1, 8, 1, 1, 1, 1, 118, 128, 128, 129, 129, 129, 129, 129, 118, 118, 118, 112, 112, 92, 92, 37, 8, 1, 1, 1, 1, 1, 1, 1, 129] 129 rigid atoms, others: [32, 33, 34, 35, 36, 7, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37]) total number of confs: 508 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054299 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054299 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054299/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054299 Building REAL250005054300 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054300' /scratch/stefan/7922901/working/building/REAL250005054300 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054300 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054300/0 /scratch/stefan/7922901/working/building/REAL250005054300 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/433 `/scratch/stefan/7922901/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC(C)(C)O1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054300.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054300 none CN(CCNC(=O)C1CC(C)(C)O1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 32, 32, 49, 49, 49, 60, 60, 60, 60, 60, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 32, 32, 32, 32, 49, 60, 60, 60, 60, 60, 60, 60, 60, 60, 1] 60 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: 199 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: REAL250005054300 none CN(CCNC(=O)C1CC(C)(C)O1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [39, 28, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 39, 57, 57, 60, 60, 60, 60, 60, 39, 39, 39, 28, 28, 19, 19, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 60] 60 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 237 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054300 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054300 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054300/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054300 Building REAL250005054301 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054301' /scratch/stefan/7922901/working/building/REAL250005054301 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054301 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054301/0 /scratch/stefan/7922901/working/building/REAL250005054301 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/434 `/scratch/stefan/7922901/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)=NO1) `REAL250005054301.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054301 none CC1CC(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 187, 187, 187, 97, 66, 26, 10, 26, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 187, 97, 97, 66, 66, 26, 26, 26, 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: 694 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: REAL250005054301 none CC1CC(C(=O)NCCN(C)C(=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.3', '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, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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 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, 46, 73, 121, 121, 182, 182, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 13, 46, 46, 73, 73, 121, 121, 121, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 729 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054301 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054301 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054301/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054301 Building REAL250005054302 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054302' /scratch/stefan/7922901/working/building/REAL250005054302 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054302 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054302/0 /scratch/stefan/7922901/working/building/REAL250005054302 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/435 `/scratch/stefan/7922901/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC(C)(F)C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054302.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054302 none CN(CCNC(=O)C1CC(C)(F)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 22, 48, 60, 101, 101, 101, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 48, 48, 60, 60, 101, 201, 201, 201, 201, 201, 201, 201, 201, 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: 678 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054302 none CN(CCNC(=O)C1CC(C)(F)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 84, 50, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 126, 191, 191, 201, 201, 201, 201, 201, 126, 126, 126, 84, 84, 50, 50, 11, 1, 1, 1, 2, 2, 2, 1, 1, 201] 201 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 37]) total number of confs: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054302 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054302 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054302/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054302 Building REAL250005054303 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054303' /scratch/stefan/7922901/working/building/REAL250005054303 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054303 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054303/0 /scratch/stefan/7922901/working/building/REAL250005054303 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/436 `/scratch/stefan/7922901/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054303.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054303 none COCC(O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 351 conformations in input total number of sets (complete confs): 351 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 93, 117, 93, 93, 63, 47, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 117, 351, 93, 63, 63, 47, 47, 14, 14, 14, 1] 351 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: 857 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054303 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054303 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054303/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054303 Building REAL250005054304 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054304' /scratch/stefan/7922901/working/building/REAL250005054304 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054304 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054304/0 /scratch/stefan/7922901/working/building/REAL250005054304 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/437 `/scratch/stefan/7922901/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC(C)(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054304.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054304 none C#CC(C)(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 201, 201, 122, 122, 69, 55, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 122, 69, 69, 55, 55, 17, 17, 17, 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: 805 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054304 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054304 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054304/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054304 Building REAL250005054305 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054305' /scratch/stefan/7922901/working/building/REAL250005054305 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054305 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054305/0 /scratch/stefan/7922901/working/building/REAL250005054305 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/438 `/scratch/stefan/7922901/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1CNC(=O)N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054305.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054305 none CN(CCNC(=O)[C@H]1CNC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.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, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 26, 26, 39, 39, 39, 64, 64, 64, 64, 64, 64, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 26, 26, 26, 26, 39, 64, 64, 64, 64, 1] 64 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054305 none CN(CCNC(=O)[C@H]1CNC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.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, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [53, 48, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 53, 62, 62, 64, 64, 64, 64, 64, 53, 53, 53, 48, 48, 36, 36, 10, 1, 1, 1, 1, 64] 64 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054305 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054305 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054305/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054305 Building REAL250005054306 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054306' /scratch/stefan/7922901/working/building/REAL250005054306 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005054306 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054306/0 /scratch/stefan/7922901/working/building/REAL250005054306 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/439 `/scratch/stefan/7922901/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN1CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054306.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054306 none CC1CCN1CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 144, 144, 144, 77, 53, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 77, 77, 53, 53, 17, 17, 17, 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: 843 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054306 none CC1CCN1CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 64, 89, 142, 142, 189, 189, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 16, 64, 64, 89, 89, 142, 142, 142, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26, 27, 28] set([6, 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, 38, 39]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054306 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054306/1 /scratch/stefan/7922901/working/building/REAL250005054306 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/440 `/scratch/stefan/7922901/working/3D/440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@@H+]1CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054306.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054306 none CC1CC[N@@H+]1CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 7, 6, 7, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 7, 7, 7, 1] 11 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: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054306 none CC1CC[N@@H+]1CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 9, 9, 10, 10, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 5, 9, 9, 9, 9, 10, 10, 10, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27, 28, 29] set([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, 37, 38, 39, 40]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054306 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `2' /scratch/stefan/7922901/working/building/REAL250005054306/2 /scratch/stefan/7922901/working/building/REAL250005054306 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 2 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/441 `/scratch/stefan/7922901/working/3D/441' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@H+]1CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054306.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005054306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054306/2/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: REAL250005054306 none CC1CC[N@H+]1CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 10, 7, 7, 7, 6, 7, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 7, 7, 7, 7, 7, 7, 7, 1] 11 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: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054306 none CC1CC[N@H+]1CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 7, 7, 7, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 7, 10, 10, 10, 10, 10, 10, 10, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27, 28, 29] set([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, 37, 38, 39, 40]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054306 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054306 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054306/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054306/1.* 2: /scratch/stefan/7922901/working/building/REAL250005054306/2.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054306 Building REAL250005054307 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054307' /scratch/stefan/7922901/working/building/REAL250005054307 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054307 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054307/0 /scratch/stefan/7922901/working/building/REAL250005054307 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/442 `/scratch/stefan/7922901/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)COC1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054307.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054307 none CN(CCNC(=O)COC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 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: [15, 6, 15, 21, 21, 43, 43, 43, 139, 176, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 21, 21, 21, 21, 43, 139, 139, 201, 201, 201, 201, 201, 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: 684 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054307 none CN(CCNC(=O)COC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 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: [193, 171, 157, 76, 76, 24, 76, 6, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 171, 171, 157, 157, 76, 24, 24, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 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, 28, 29, 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/7922901/working/building/REAL250005054307 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054307 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054307/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054307 Building REAL250005054308 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054308' /scratch/stefan/7922901/working/building/REAL250005054308 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054308 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054308/0 /scratch/stefan/7922901/working/building/REAL250005054308 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/443 `/scratch/stefan/7922901/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NC=CN1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054308.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054308 none CN(CCNC(=O)C1=NC=CN1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 1] 17 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: 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: REAL250005054308 none CN(CCNC(=O)C1=NC=CN1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 17, 19, 19, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 12, 12, 4, 1, 1, 1, 19] 19 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054308 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054308 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054308/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054308 Building REAL250005054309 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054309' /scratch/stefan/7922901/working/building/REAL250005054309 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054309 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054309/0 /scratch/stefan/7922901/working/building/REAL250005054309 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/444 `/scratch/stefan/7922901/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C=CC1CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054309.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054309 none CN(CCNC(=O)C=CC1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 18, 37, 49, 66, 66, 66, 136, 136, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 18, 18, 18, 37, 37, 49, 49, 66, 136, 136, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005054309 none CN(CCNC(=O)C=CC1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 100, 70, 26, 26, 7, 26, 7, 1, 1, 1, 1, 1, 118, 181, 181, 201, 201, 201, 201, 201, 118, 118, 118, 100, 100, 70, 70, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054309 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054309 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054309/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054309 Building REAL250005054310 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054310' /scratch/stefan/7922901/working/building/REAL250005054310 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054310 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054310/0 /scratch/stefan/7922901/working/building/REAL250005054310 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/445 `/scratch/stefan/7922901/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054310.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054310 none CCCC=CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 93, 93, 40, 40, 40, 34, 28, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 163, 163, 93, 93, 40, 34, 34, 28, 28, 15, 15, 15, 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: 938 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054310 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054310 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054310/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054310 Building REAL250005054311 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054311' /scratch/stefan/7922901/working/building/REAL250005054311 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054311 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054311/0 /scratch/stefan/7922901/working/building/REAL250005054311 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/446 `/scratch/stefan/7922901/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054311.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054311 none CC=C(F)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 184, 201, 184, 184, 112, 84, 32, 11, 32, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 184, 112, 112, 84, 84, 32, 32, 32, 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: 757 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054311 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054311 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054311/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054311 Building REAL250005054312 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054312' /scratch/stefan/7922901/working/building/REAL250005054312 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054312 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054312/0 /scratch/stefan/7922901/working/building/REAL250005054312 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/447 `/scratch/stefan/7922901/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005054312.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054312 none CCC(C(=O)NCCN(C)C(=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.3', '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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 179, 114, 114, 114, 83, 63, 29, 12, 29, 1, 12, 1, 1, 1, 1, 1, 1, 178, 201, 200, 185, 185, 185, 185, 185, 179, 114, 83, 83, 63, 63, 29, 29, 29, 1, 201, 201, 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, 41, 42]) total number of confs: 943 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054312 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054312 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054312/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054312 Building REAL250005054313 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054313' /scratch/stefan/7922901/working/building/REAL250005054313 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054313 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054313/0 /scratch/stefan/7922901/working/building/REAL250005054313 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/448 `/scratch/stefan/7922901/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(F)=C1CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054313.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054313 none CN(CCNC(=O)C(F)=C1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 8, 23, 43, 47, 88, 88, 88, 133, 133, 133, 133, 133, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 43, 43, 47, 47, 88, 133, 133, 133, 133, 133, 133, 1] 133 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: 453 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: REAL250005054313 none CN(CCNC(=O)C(F)=C1CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [103, 78, 50, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 103, 130, 130, 133, 133, 133, 133, 133, 103, 103, 103, 78, 78, 50, 50, 9, 1, 1, 1, 1, 1, 1, 133] 133 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 530 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054313 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054313 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054313/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054313 Building REAL250005054314 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054314' /scratch/stefan/7922901/working/building/REAL250005054314 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054314 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054314/0 /scratch/stefan/7922901/working/building/REAL250005054314 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/449 `/scratch/stefan/7922901/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054314.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054314 none CCC(CO)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [176, 153, 86, 153, 196, 86, 86, 40, 38, 19, 10, 19, 1, 10, 1, 1, 1, 1, 1, 1, 185, 185, 185, 185, 185, 153, 196, 196, 588, 86, 40, 40, 38, 38, 19, 19, 19, 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: 1658 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054314 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054314 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054314/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054314 Building REAL250005054315 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054315' /scratch/stefan/7922901/working/building/REAL250005054315 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054315 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054315/0 /scratch/stefan/7922901/working/building/REAL250005054315 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/450 `/scratch/stefan/7922901/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054315.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054315 none CC(CO)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 111, 195, 201, 111, 111, 66, 50, 22, 10, 22, 1, 10, 1, 1, 1, 1, 1, 1, 195, 195, 195, 195, 201, 201, 603, 111, 66, 66, 50, 50, 22, 22, 22, 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: 1428 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054315 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054315 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054315/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054315 Building REAL250005054316 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054316' /scratch/stefan/7922901/working/building/REAL250005054316 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054316 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054316/0 /scratch/stefan/7922901/working/building/REAL250005054316 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/451 `/scratch/stefan/7922901/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CON=C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054316.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054316 none CN(CCNC(=O)C1=CON=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 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: [22, 8, 22, 43, 53, 73, 73, 73, 129, 129, 129, 129, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 43, 43, 53, 53, 73, 129, 129, 1] 129 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: 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: REAL250005054316 none CN(CCNC(=O)C1=CON=C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 8, 1, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 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: [77, 45, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 77, 123, 123, 129, 129, 129, 129, 129, 77, 77, 77, 45, 45, 25, 25, 5, 1, 1, 129] 129 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/7922901/working/building/REAL250005054316 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054316 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054316/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054316 Building REAL250005054317 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054317' /scratch/stefan/7922901/working/building/REAL250005054317 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054317 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054317/0 /scratch/stefan/7922901/working/building/REAL250005054317 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/452 `/scratch/stefan/7922901/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1C[C@H]1CF)C(=O)C1=CC(=O)[N-]O1) `REAL250005054317.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054317 none CN(CCNC(=O)[C@@H]1C[C@H]1CF)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 18, 34, 38, 68, 68, 68, 192, 192, 192, 192, 192, 201, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 34, 34, 38, 38, 68, 192, 192, 201, 201, 1] 201 rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 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: REAL250005054317 none CN(CCNC(=O)[C@@H]1C[C@H]1CF)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 100, 67, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 10, 147, 185, 185, 192, 192, 192, 192, 192, 147, 147, 147, 100, 100, 67, 67, 13, 1, 1, 10, 10, 192] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 774 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054317 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054317 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054317/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054317 Building REAL250005054318 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054318' /scratch/stefan/7922901/working/building/REAL250005054318 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054318 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054318/0 /scratch/stefan/7922901/working/building/REAL250005054318 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/453 `/scratch/stefan/7922901/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054318.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054318 none C#CC1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 84, 84, 84, 60, 48, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 84, 60, 60, 48, 48, 18, 18, 18, 1, 201, 201, 201, 201] 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, 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: REAL250005054318 none C#CC1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7, 7, 39, 63, 105, 105, 195, 195, 201, 201, 201, 201, 201, 1, 1, 1, 7, 39, 39, 63, 63, 105, 105, 105, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 32, 18, 19, 20, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054318 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054318 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054318/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054318 Building REAL250005054319 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054319' /scratch/stefan/7922901/working/building/REAL250005054319 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054319 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054319/0 /scratch/stefan/7922901/working/building/REAL250005054319 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/454 `/scratch/stefan/7922901/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=COCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054319.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054319 none CN(CCNC(=O)C1=COCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 22, 43, 51, 67, 67, 67, 105, 105, 105, 105, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 43, 43, 51, 51, 67, 105, 105, 105, 105, 105, 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: 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: REAL250005054319 none CN(CCNC(=O)C1=COCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [70, 58, 41, 11, 11, 1, 11, 1, 1, 1, 1, 1, 70, 103, 103, 105, 105, 105, 105, 105, 70, 70, 70, 58, 58, 41, 41, 11, 1, 1, 1, 1, 1, 105] 105 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054319 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054319 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054319/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054319 Building REAL250005054320 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054320' /scratch/stefan/7922901/working/building/REAL250005054320 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054320 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054320/0 /scratch/stefan/7922901/working/building/REAL250005054320 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/455 `/scratch/stefan/7922901/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054320.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054320 none C[C@H](O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 178, 201, 201, 178, 178, 105, 71, 23, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 603, 178, 105, 105, 71, 71, 23, 23, 23, 1] 603 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 1413 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054320 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054320 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054320/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054320 Building REAL250005054321 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054321' /scratch/stefan/7922901/working/building/REAL250005054321 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054321 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054321/0 /scratch/stefan/7922901/working/building/REAL250005054321 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/456 `/scratch/stefan/7922901/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(F)=NN1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054321.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054321 none CN(CCNC(=O)C1=CC(F)=NN1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 15, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 19, 19, 23, 23, 23, 34, 34, 34, 34, 34, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 19, 19, 19, 19, 23, 34, 34, 1] 34 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: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054321 none CN(CCNC(=O)C1=CC(F)=NN1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'C.2', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 15, 8, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 28, 34, 34, 34, 34, 34, 34, 34, 28, 28, 28, 25, 25, 18, 18, 7, 1, 1, 34] 34 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054321 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054321 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054321/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054321 Building REAL250005054322 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054322' /scratch/stefan/7922901/working/building/REAL250005054322 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054322 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054322/0 /scratch/stefan/7922901/working/building/REAL250005054322 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/457 `/scratch/stefan/7922901/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1C=CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054322.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054322 none CN(CCNC(=O)C1C=CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 9, 25, 47, 51, 84, 84, 84, 173, 173, 173, 173, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 47, 47, 51, 51, 84, 173, 173, 173, 173, 173, 173, 173, 1] 173 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: 562 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054322 none CN(CCNC(=O)C1C=CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [124, 86, 53, 11, 11, 1, 11, 1, 1, 1, 1, 1, 124, 169, 169, 173, 173, 173, 173, 173, 124, 124, 124, 86, 86, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 173] 173 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054322 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054322 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054322/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054322 Building REAL250005054323 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054323' /scratch/stefan/7922901/working/building/REAL250005054323 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054323 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054323/0 /scratch/stefan/7922901/working/building/REAL250005054323 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/458 `/scratch/stefan/7922901/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054323.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054323 none CC(O)C(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 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, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 180, 201, 110, 180, 110, 110, 65, 50, 19, 9, 19, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 180, 180, 180, 180, 110, 65, 65, 50, 50, 19, 19, 19, 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: 1447 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054323 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054323 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054323/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054323 Building REAL250005054324 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054324' /scratch/stefan/7922901/working/building/REAL250005054324 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054324 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054324/0 /scratch/stefan/7922901/working/building/REAL250005054324 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/459 `/scratch/stefan/7922901/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(O)CCOC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054324.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054324 none CN(CCNC(=O)C1(O)CCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 3, 7, 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 270 conformations in input total number of sets (complete confs): 270 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 21, 28, 28, 53, 53, 53, 90, 90, 90, 90, 90, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 28, 28, 28, 28, 53, 270, 90, 90, 90, 90, 90, 90, 1] 270 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: 559 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054324 none CN(CCNC(=O)C1(O)CCOC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 3, 7, 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 270 conformations in input total number of sets (complete confs): 270 using faster count positions algorithm for large data unique positions, atoms: [72, 58, 43, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 72, 90, 90, 90, 90, 90, 90, 90, 72, 72, 72, 58, 58, 43, 43, 10, 6, 1, 1, 1, 1, 1, 1, 90] 270 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 357 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054324 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054324 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054324/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054324 Building REAL250005054325 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054325' /scratch/stefan/7922901/working/building/REAL250005054325 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054325 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054325/0 /scratch/stefan/7922901/working/building/REAL250005054325 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/460 `/scratch/stefan/7922901/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054325.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054325 none C=C1CC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 102, 102, 102, 63, 48, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 102, 63, 63, 48, 48, 17, 17, 17, 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: 670 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054325 none C=C1CC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 60, 91, 134, 134, 192, 192, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 60, 60, 91, 91, 134, 134, 134, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 768 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054325 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054325 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054325/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054325 Building REAL250005054326 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054326' /scratch/stefan/7922901/working/building/REAL250005054326 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054326 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054326/0 /scratch/stefan/7922901/working/building/REAL250005054326 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/461 `/scratch/stefan/7922901/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1CC=CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054326.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054326 none CN(CCNC(=O)CC1CC=CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 30, 33, 60, 60, 60, 184, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 30, 30, 33, 33, 60, 184, 184, 201, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005054326 none CN(CCNC(=O)CC1CC=CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 142, 100, 31, 31, 6, 31, 1, 1, 1, 1, 1, 1, 171, 200, 200, 201, 201, 201, 201, 201, 171, 171, 171, 142, 142, 100, 100, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38]) total number of confs: 836 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054326 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054326 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054326/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054326 Building REAL250005054327 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054327' /scratch/stefan/7922901/working/building/REAL250005054327 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054327 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054327/0 /scratch/stefan/7922901/working/building/REAL250005054327 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/462 `/scratch/stefan/7922901/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054327.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054327 none CC(CF)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 127, 196, 201, 127, 127, 77, 55, 22, 10, 22, 1, 10, 1, 1, 1, 1, 1, 1, 196, 196, 196, 196, 201, 201, 127, 77, 77, 55, 55, 22, 22, 22, 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: 806 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054327 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054327 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054327/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054327 Building REAL250005054328 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054328' /scratch/stefan/7922901/working/building/REAL250005054328 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054328 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054328/0 /scratch/stefan/7922901/working/building/REAL250005054328 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/463 `/scratch/stefan/7922901/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(C)(C)C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054328.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054328 none CN(CCNC(=O)C1=CC(C)(C)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 10, 30, 60, 82, 147, 147, 147, 148, 148, 148, 148, 148, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 60, 60, 82, 82, 147, 148, 148, 148, 148, 148, 148, 148, 148, 148, 1] 148 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: 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: REAL250005054328 none CN(CCNC(=O)C1=CC(C)(C)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [94, 58, 35, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 94, 142, 142, 148, 148, 148, 148, 148, 94, 94, 94, 58, 58, 35, 35, 9, 1, 2, 2, 2, 2, 2, 2, 1, 1, 148] 148 rigid atoms, others: [36, 5, 7, 8, 9, 10, 11, 12, 29, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054328 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054328 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054328/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054328 Building REAL250005054329 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054329' /scratch/stefan/7922901/working/building/REAL250005054329 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054329 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054329/0 /scratch/stefan/7922901/working/building/REAL250005054329 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/464 `/scratch/stefan/7922901/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1CC1(F)F)C(=O)C1=CC(=O)[N-]O1) `REAL250005054329.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054329 none CN(CCNC(=O)[C@@H]1CC1(F)F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 8, 23, 46, 55, 95, 95, 95, 173, 173, 173, 173, 173, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 46, 46, 55, 55, 95, 173, 173, 1] 173 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: 585 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054329 none CN(CCNC(=O)[C@@H]1CC1(F)F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [133, 91, 59, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 133, 172, 172, 173, 173, 173, 173, 173, 133, 133, 133, 91, 91, 59, 59, 13, 1, 1, 173] 173 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 682 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054329 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054329 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054329/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054329 Building REAL250005054330 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054330' /scratch/stefan/7922901/working/building/REAL250005054330 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054330 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054330/0 /scratch/stefan/7922901/working/building/REAL250005054330 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/465 `/scratch/stefan/7922901/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054330.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054330 none CC(=O)NCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [189, 187, 189, 189, 187, 101, 101, 101, 67, 51, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 191, 191, 189, 189, 101, 67, 67, 51, 51, 16, 16, 16, 1] 191 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: 863 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054330 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054330 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054330/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054330 Building REAL250005054331 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054331' /scratch/stefan/7922901/working/building/REAL250005054331 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054331 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054331/0 /scratch/stefan/7922901/working/building/REAL250005054331 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/466 `/scratch/stefan/7922901/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CNC(=O)N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054331.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054331 none CN(CCNC(=O)C1=CNC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 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 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 18, 35, 39, 57, 57, 57, 81, 81, 81, 81, 81, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 35, 35, 39, 39, 57, 81, 81, 81, 1] 81 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: 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: REAL250005054331 none CN(CCNC(=O)C1=CNC(=O)N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 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 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [63, 47, 34, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 63, 81, 81, 81, 81, 81, 81, 81, 63, 63, 63, 47, 47, 34, 34, 8, 1, 1, 1, 81] 81 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054331 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054331 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054331/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054331 Building REAL250005054332 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054332' /scratch/stefan/7922901/working/building/REAL250005054332 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054332 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054332/0 /scratch/stefan/7922901/working/building/REAL250005054332 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/467 `/scratch/stefan/7922901/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054332.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054332 none CC1CCCC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 114, 114, 114, 64, 54, 20, 8, 20, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 114, 64, 64, 54, 54, 20, 20, 20, 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: 670 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054332 none CC1CCCC1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 39, 65, 103, 103, 183, 183, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 39, 39, 65, 65, 103, 103, 103, 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: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054332 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054332 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054332/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054332 Building REAL250005054333 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054333' /scratch/stefan/7922901/working/building/REAL250005054333 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054333 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054333/0 /scratch/stefan/7922901/working/building/REAL250005054333 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/468 `/scratch/stefan/7922901/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054333.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054333 none C=C(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 201, 89, 89, 89, 66, 48, 21, 8, 21, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 199, 89, 66, 66, 48, 48, 21, 21, 21, 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: 817 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054333 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054333 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054333/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054333 Building REAL250005054334 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054334' /scratch/stefan/7922901/working/building/REAL250005054334 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054334 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054334/0 /scratch/stefan/7922901/working/building/REAL250005054334 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/469 `/scratch/stefan/7922901/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054334.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054334 none CCSCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 159, 83, 83, 83, 61, 53, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 159, 159, 83, 61, 61, 53, 53, 17, 17, 17, 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.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054334 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054334 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054334/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054334 Building REAL250005054335 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054335' /scratch/stefan/7922901/working/building/REAL250005054335 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054335 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054335/0 /scratch/stefan/7922901/working/building/REAL250005054335 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/470 `/scratch/stefan/7922901/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054335.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054335 none CC(C)=C(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 144, 201, 144, 144, 86, 59, 23, 9, 23, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 86, 86, 59, 59, 23, 23, 23, 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: 763 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054335 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054335 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054335/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054335 Building REAL250005054336 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054336' /scratch/stefan/7922901/working/building/REAL250005054336 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054336 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054336/0 /scratch/stefan/7922901/working/building/REAL250005054336 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/471 `/scratch/stefan/7922901/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054336.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054336 none CCCC(O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 146, 115, 146, 115, 115, 70, 47, 17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 146, 438, 115, 70, 70, 47, 47, 17, 17, 17, 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: 1390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054336 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054336 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054336/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054336 Building REAL250005054337 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054337' /scratch/stefan/7922901/working/building/REAL250005054337 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054337 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054337/0 /scratch/stefan/7922901/working/building/REAL250005054337 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/472 `/scratch/stefan/7922901/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054337.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054337 none CCCCC(O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 128, 96, 128, 96, 96, 54, 38, 16, 7, 16, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 384, 96, 54, 54, 38, 38, 16, 16, 16, 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: 1356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054337 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054337 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054337/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054337 Building REAL250005054338 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054338' /scratch/stefan/7922901/working/building/REAL250005054338 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054338 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054338/0 /scratch/stefan/7922901/working/building/REAL250005054338 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/473 `/scratch/stefan/7922901/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CSC1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054338.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054338 none CN(CCNC(=O)CSC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 14, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 15, 21, 21, 41, 41, 41, 103, 153, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 21, 21, 21, 21, 41, 103, 103, 201, 201, 201, 201, 201, 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: 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: REAL250005054338 none CN(CCNC(=O)CSC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 14, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 171, 154, 66, 66, 25, 66, 6, 1, 1, 1, 1, 190, 201, 201, 201, 201, 201, 201, 201, 190, 190, 190, 171, 171, 154, 154, 66, 25, 25, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 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, 28, 29, 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/7922901/working/building/REAL250005054338 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054338 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054338/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054338 Building REAL250005054339 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054339' /scratch/stefan/7922901/working/building/REAL250005054339 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054339 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054339/0 /scratch/stefan/7922901/working/building/REAL250005054339 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/474 `/scratch/stefan/7922901/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054339.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054339 none CCC(O)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 414 conformations in input total number of sets (complete confs): 414 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 132, 138, 68, 68, 68, 52, 37, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 138, 138, 414, 132, 132, 68, 52, 52, 37, 37, 14, 14, 14, 1] 414 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: 1028 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054339 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054339 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054339/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054339 Building REAL250005054340 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054340' /scratch/stefan/7922901/working/building/REAL250005054340 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054340 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054340/0 /scratch/stefan/7922901/working/building/REAL250005054340 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/475 `/scratch/stefan/7922901/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(Cl)=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054340.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054340 none CC(Cl)=CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 16, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 136, 136, 86, 65, 22, 10, 22, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 136, 86, 86, 65, 65, 22, 22, 22, 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: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054340 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054340 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054340/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054340 Building REAL250005054341 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054341' /scratch/stefan/7922901/working/building/REAL250005054341 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054341 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054341/0 /scratch/stefan/7922901/working/building/REAL250005054341 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/476 `/scratch/stefan/7922901/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054341.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054341 none CC=CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 138, 138, 138, 99, 71, 26, 10, 26, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 138, 99, 99, 71, 71, 26, 26, 26, 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/7922901/working/building/REAL250005054341 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054341 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054341/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054341 Building REAL250005054342 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054342' /scratch/stefan/7922901/working/building/REAL250005054342 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054342 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054342/0 /scratch/stefan/7922901/working/building/REAL250005054342 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/477 `/scratch/stefan/7922901/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)(F)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054342.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054342 none CCC(F)(F)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 183, 83, 183, 183, 83, 83, 37, 31, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 83, 37, 37, 31, 31, 15, 15, 15, 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: 903 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054342 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054342 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054342/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054342 Building REAL250005054343 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054343' /scratch/stefan/7922901/working/building/REAL250005054343 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054343 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054343/0 /scratch/stefan/7922901/working/building/REAL250005054343 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/478 `/scratch/stefan/7922901/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(C)CC1F)C(=O)C1=CC(=O)[N-]O1) `REAL250005054343.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054343 none CN(CCNC(=O)C1(C)CC1F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 52, 65, 97, 97, 97, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 52, 52, 65, 65, 97, 201, 201, 201, 201, 201, 201, 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: 653 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: REAL250005054343 none CN(CCNC(=O)C1(C)CC1F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 63, 35, 6, 6, 1, 6, 1, 1, 1, 1, 1, 111, 186, 186, 201, 201, 201, 201, 201, 111, 111, 111, 63, 63, 35, 35, 6, 2, 2, 2, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 737 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054343 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054343 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054343/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054343 Building REAL250005054344 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054344' /scratch/stefan/7922901/working/building/REAL250005054344 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054344 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054344/0 /scratch/stefan/7922901/working/building/REAL250005054344 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/479 `/scratch/stefan/7922901/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H]1C[C@@H](O)C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054344.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054344 none CN(CCNC(=O)[C@H]1C[C@@H](O)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 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: [26, 7, 26, 51, 63, 107, 107, 107, 201, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 26, 26, 26, 51, 51, 63, 63, 107, 201, 201, 603, 201, 201, 1] 603 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: 1280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054344 none CN(CCNC(=O)[C@H]1C[C@@H](O)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', '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, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 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: [130, 86, 51, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 130, 194, 194, 201, 201, 201, 201, 201, 130, 130, 130, 86, 86, 51, 51, 11, 1, 1, 3, 1, 1, 201] 603 rigid atoms, others: [33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054344 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054344 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054344/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054344 Building REAL250005054345 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054345' /scratch/stefan/7922901/working/building/REAL250005054345 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054345 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054345/0 /scratch/stefan/7922901/working/building/REAL250005054345 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/480 `/scratch/stefan/7922901/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1CC1(C)C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054345.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054345 none CN(CCNC(=O)CC1CC1(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 15, 29, 33, 58, 58, 58, 187, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 29, 29, 33, 33, 58, 187, 187, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 774 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054345 none CN(CCNC(=O)CC1CC1(C)C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 155, 121, 36, 36, 5, 36, 1, 1, 1, 1, 1, 1, 179, 200, 200, 201, 201, 201, 201, 201, 179, 179, 179, 154, 155, 121, 121, 36, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 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: 829 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054345 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054345 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054345/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054345 Building REAL250005054346 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054346' /scratch/stefan/7922901/working/building/REAL250005054346 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054346 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054346/0 /scratch/stefan/7922901/working/building/REAL250005054346 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/481 `/scratch/stefan/7922901/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(N)=O)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054346.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054346 none CC(NC(N)=O)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 55, 75, 75, 75, 75, 55, 55, 34, 27, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 75, 55, 34, 34, 27, 27, 13, 13, 13, 1] 75 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: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054346 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054346 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054346/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054346 Building REAL250005054347 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054347' /scratch/stefan/7922901/working/building/REAL250005054347 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054347 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054347/0 /scratch/stefan/7922901/working/building/REAL250005054347 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/482 `/scratch/stefan/7922901/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054347.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054347 none C=C(C)CCCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 115, 24, 24, 24, 22, 18, 10, 6, 10, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 145, 145, 117, 117, 24, 22, 22, 18, 18, 10, 10, 10, 1] 201 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1022 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054347 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054347 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054347/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054347 Building REAL250005054348 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054348' /scratch/stefan/7922901/working/building/REAL250005054348 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054348 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054348/0 /scratch/stefan/7922901/working/building/REAL250005054348 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/483 `/scratch/stefan/7922901/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(C)CC(F)C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054348.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054348 none CN(CCNC(=O)C1(C)CC(F)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 59, 69, 107, 107, 107, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 27, 27, 27, 59, 59, 69, 69, 107, 201, 201, 201, 201, 201, 201, 201, 201, 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: 667 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054348 none CN(CCNC(=O)C1(C)CC(F)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 61, 34, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 106, 188, 188, 201, 201, 201, 201, 201, 106, 106, 106, 61, 61, 34, 34, 6, 2, 2, 2, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37]) total number of confs: 719 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054348 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054348 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054348/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054348 Building REAL250005054349 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054349' /scratch/stefan/7922901/working/building/REAL250005054349 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054349 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054349/0 /scratch/stefan/7922901/working/building/REAL250005054349 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/484 `/scratch/stefan/7922901/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054349.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054349 none C[C@@H]1C[C@H]1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 201, 99, 99, 64, 49, 17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 99, 64, 64, 49, 49, 17, 17, 17, 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: 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: REAL250005054349 none C[C@@H]1C[C@H]1C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 73, 115, 115, 188, 188, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 12, 44, 44, 73, 73, 115, 115, 115, 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: 736 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054349 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054349 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054349/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054349 Building REAL250005054350 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054350' /scratch/stefan/7922901/working/building/REAL250005054350 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054350 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054350/0 /scratch/stefan/7922901/working/building/REAL250005054350 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/485 `/scratch/stefan/7922901/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1CC[C@@H]2C[C@@H]21)C(=O)C1=CC(=O)[N-]O1) `REAL250005054350.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054350 none CN(CCNC(=O)[C@@H]1CC[C@@H]2C[C@@H]21)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 20, 47, 58, 91, 91, 91, 201, 201, 201, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 47, 47, 58, 58, 91, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 679 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: REAL250005054350 none CN(CCNC(=O)[C@@H]1CC[C@@H]2C[C@@H]21)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 98, 64, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 143, 194, 194, 201, 201, 201, 201, 201, 143, 143, 143, 98, 98, 64, 64, 13, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 37] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 792 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054350 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054350 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054350/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054350 Building REAL250005054351 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054351' /scratch/stefan/7922901/working/building/REAL250005054351 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054351 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054351/0 /scratch/stefan/7922901/working/building/REAL250005054351 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/486 `/scratch/stefan/7922901/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)COC1COC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054351.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054351 none CN(CCNC(=O)COC1COC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 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, 10, 16, 16, 33, 33, 33, 122, 169, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 16, 16, 16, 16, 33, 122, 122, 201, 201, 201, 201, 201, 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: 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: REAL250005054351 none CN(CCNC(=O)COC1COC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 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, 181, 170, 88, 88, 26, 88, 6, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 201, 201, 201, 199, 199, 199, 181, 181, 170, 170, 88, 26, 26, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/7922901/working/building/REAL250005054351 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054351 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054351/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054351 Building REAL250005054352 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054352' /scratch/stefan/7922901/working/building/REAL250005054352 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054352 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054352/0 /scratch/stefan/7922901/working/building/REAL250005054352 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/487 `/scratch/stefan/7922901/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@]2(C(=O)NCCN(C)C(=O)C3=CC(=O)[N-]O3)C[C@H]12) `REAL250005054352.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054352 none C[C@@H]1C[C@]2(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 74, 74, 74, 56, 46, 18, 8, 18, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 74, 56, 56, 46, 46, 18, 18, 18, 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: 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: REAL250005054352 none C[C@@H]1C[C@]2(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 60, 99, 99, 180, 180, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 7, 34, 34, 60, 60, 99, 99, 99, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 26, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054352 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054352 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054352/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054352 Building REAL250005054353 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054353' /scratch/stefan/7922901/working/building/REAL250005054353 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054353 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054353/0 /scratch/stefan/7922901/working/building/REAL250005054353 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/488 `/scratch/stefan/7922901/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054353.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054353 none CNC(=O)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 123, 133, 85, 85, 85, 53, 39, 14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 123, 123, 85, 53, 53, 39, 39, 14, 14, 14, 1] 133 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: 541 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054353 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054353 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054353/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054353 Building REAL250005054354 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054354' /scratch/stefan/7922901/working/building/REAL250005054354 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054354 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054354/0 /scratch/stefan/7922901/working/building/REAL250005054354 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/489 `/scratch/stefan/7922901/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC=CCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054354.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054354 none C=CC=CCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 148, 89, 89, 89, 65, 45, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 148, 148, 89, 65, 65, 45, 45, 16, 16, 16, 1] 164 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: 683 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054354 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054354 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054354/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054354 Building REAL250005054355 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054355' /scratch/stefan/7922901/working/building/REAL250005054355 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054355 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054355/0 /scratch/stefan/7922901/working/building/REAL250005054355 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/490 `/scratch/stefan/7922901/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005054355.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054355 none C#CC1(C(=O)NCCN(C)C(=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.3', '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: [1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 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, 93, 93, 93, 64, 54, 19, 8, 19, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 93, 64, 64, 54, 54, 19, 19, 19, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 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: REAL250005054355 none C#CC1(C(=O)NCCN(C)C(=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.3', '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: [1, 1, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 33, 57, 95, 95, 186, 186, 201, 201, 201, 201, 201, 1, 1, 1, 1, 7, 33, 33, 57, 57, 95, 95, 95, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 36, 33, 35, 32, 34, 18, 19, 20, 21, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054355 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054355 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054355/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054355 Building REAL250005054356 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054356' /scratch/stefan/7922901/working/building/REAL250005054356 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005054356 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054356/0 /scratch/stefan/7922901/working/building/REAL250005054356 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/491 `/scratch/stefan/7922901/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1CCC[N@@H+]1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054356.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054356 none CN(CCNC(=O)[C@@H]1CCC[N@@H+]1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 8, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 1, 6, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 12 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: 35 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: REAL250005054356 none CN(CCNC(=O)[C@@H]1CCC[N@@H+]1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 11, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 8, 8, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12] 12 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40]) total number of confs: 56 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054356 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054356/1 /scratch/stefan/7922901/working/building/REAL250005054356 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/492 `/scratch/stefan/7922901/working/3D/492' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1CCC[N@H+]1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054356.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054356 none CN(CCNC(=O)[C@@H]1CCC[N@H+]1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 7, 7, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 12 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: 33 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: REAL250005054356 none CN(CCNC(=O)[C@@H]1CCC[N@H+]1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12] 12 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40]) total number of confs: 47 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054356 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `2' /scratch/stefan/7922901/working/building/REAL250005054356/2 /scratch/stefan/7922901/working/building/REAL250005054356 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 2 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/493 `/scratch/stefan/7922901/working/3D/493' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@H]1CCCN1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054356.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005054356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054356/2/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: REAL250005054356 none CN(CCNC(=O)[C@@H]1CCCN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 8, 23, 32, 32, 58, 58, 58, 112, 112, 112, 112, 112, 112, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 32, 32, 32, 32, 58, 112, 112, 112, 112, 112, 112, 112, 112, 112, 1] 112 rigid atoms, others: [39, 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]) total number of confs: 341 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: REAL250005054356 none CN(CCNC(=O)[C@@H]1CCCN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 10, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [89, 72, 53, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 89, 112, 112, 112, 112, 112, 112, 112, 89, 89, 89, 72, 72, 53, 53, 13, 1, 1, 1, 1, 1, 1, 2, 2, 2, 112] 112 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39]) total number of confs: 449 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054356 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054356 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054356/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054356/1.* 2: /scratch/stefan/7922901/working/building/REAL250005054356/2.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054356 Building REAL250005054357 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054357' /scratch/stefan/7922901/working/building/REAL250005054357 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054357 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054357/0 /scratch/stefan/7922901/working/building/REAL250005054357 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/494 `/scratch/stefan/7922901/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1CC=CCO1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054357.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054357 none CN(CCNC(=O)C1CC=CCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 27, 27, 50, 50, 50, 97, 97, 97, 97, 97, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 27, 27, 27, 27, 50, 97, 97, 97, 97, 97, 97, 97, 1] 97 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: 305 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: REAL250005054357 none CN(CCNC(=O)C1CC=CCO1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [74, 63, 47, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 74, 96, 96, 97, 97, 97, 97, 97, 74, 74, 74, 63, 63, 47, 47, 13, 1, 1, 1, 1, 1, 1, 1, 97] 97 rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 385 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054357 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054357 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054357/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054357 Building REAL250005054358 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054358' /scratch/stefan/7922901/working/building/REAL250005054358 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054358 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054358/0 /scratch/stefan/7922901/working/building/REAL250005054358 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/495 `/scratch/stefan/7922901/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCOC1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054358.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054358 none CN(CCNC(=O)CCOC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 13, 20, 20, 34, 34, 34, 93, 112, 148, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 13, 13, 13, 20, 20, 20, 20, 34, 93, 93, 112, 112, 201, 201, 201, 201, 201, 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: REAL250005054358 none CN(CCNC(=O)CCOC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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: [179, 160, 131, 83, 83, 29, 83, 18, 6, 1, 1, 1, 1, 178, 201, 201, 201, 201, 201, 201, 201, 179, 179, 179, 160, 160, 131, 131, 83, 29, 29, 18, 18, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 842 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054358 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054358 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054358/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054358 Building REAL250005054359 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054359' /scratch/stefan/7922901/working/building/REAL250005054359 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054359 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054359/0 /scratch/stefan/7922901/working/building/REAL250005054359 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/496 `/scratch/stefan/7922901/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCCCCO)C(=O)C1=CC(=O)[N-]O1) `REAL250005054359.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054359 none CN(CCNC(=O)CCCCCO)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 6, 13, 28, 28, 34, 34, 34, 114, 153, 177, 181, 201, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 28, 28, 28, 28, 34, 114, 114, 173, 173, 177, 177, 201, 201, 191, 191, 603, 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: 1733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054359 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054359 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054359/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054359 Building REAL250005054360 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054360' /scratch/stefan/7922901/working/building/REAL250005054360 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054360 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054360/0 /scratch/stefan/7922901/working/building/REAL250005054360 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/497 `/scratch/stefan/7922901/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CSC=N1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054360.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054360 none CN(CCNC(=O)C1=CSC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [20, 6, 20, 31, 33, 53, 53, 53, 75, 75, 75, 75, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 31, 31, 33, 33, 53, 75, 75, 1] 75 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: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054360 none CN(CCNC(=O)C1=CSC=N1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [61, 51, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 61, 75, 75, 75, 75, 75, 75, 75, 61, 61, 61, 51, 51, 37, 37, 11, 1, 1, 75] 75 rigid atoms, others: [5, 7, 8, 9, 10, 11, 28, 29] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054360 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054360 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054360/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054360 Building REAL250005054361 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054361' /scratch/stefan/7922901/working/building/REAL250005054361 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054361 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054361/0 /scratch/stefan/7922901/working/building/REAL250005054361 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/498 `/scratch/stefan/7922901/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(CO)CCC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054361.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054361 none CN(CCNC(=O)C1(CO)CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 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: [18, 6, 18, 32, 37, 71, 71, 71, 160, 201, 160, 160, 160, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 32, 32, 37, 37, 71, 201, 201, 603, 160, 160, 160, 160, 160, 160, 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: 1362 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054361 none CN(CCNC(=O)C1(CO)CCC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 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: [102, 59, 35, 7, 7, 1, 7, 1, 1, 10, 1, 1, 1, 102, 151, 151, 160, 160, 160, 160, 160, 102, 102, 102, 59, 59, 35, 35, 7, 10, 10, 30, 1, 1, 1, 1, 1, 1, 160] 603 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 10, 11, 12, 37] set([0, 1, 2, 3, 4, 6, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 650 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054361 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054361 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054361/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054361 Building REAL250005054362 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054362' /scratch/stefan/7922901/working/building/REAL250005054362 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054362 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054362/0 /scratch/stefan/7922901/working/building/REAL250005054362 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/499 `/scratch/stefan/7922901/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CCC(N)=O)C(=O)C1=CC(=O)[N-]O1) `REAL250005054362.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054362 none CN(CCNC(=O)CCC(N)=O)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', 'O.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 1, 8, 11, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 6, 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: [17, 6, 17, 31, 33, 59, 59, 59, 157, 191, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 31, 31, 33, 33, 59, 157, 157, 191, 191, 201, 201, 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: 853 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054362 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054362 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054362/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054362 Building REAL250005054363 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054363' /scratch/stefan/7922901/working/building/REAL250005054363 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054363 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054363/0 /scratch/stefan/7922901/working/building/REAL250005054363 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/500 `/scratch/stefan/7922901/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NCCN(C)C(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054363.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054363 none C=CCC1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 177, 81, 81, 81, 69, 46, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 177, 177, 200, 200, 200, 200, 200, 81, 69, 69, 46, 46, 17, 17, 17, 1, 177, 177, 177, 177] 200 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: 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: REAL250005054363 none C=CCC1(C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [16, 4, 1, 1, 1, 6, 6, 6, 26, 34, 64, 64, 151, 151, 177, 177, 177, 177, 177, 1, 1, 16, 16, 16, 4, 4, 6, 26, 26, 34, 34, 64, 64, 64, 177, 1, 1, 1, 1] 200 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: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054363 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054363 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054363/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054363 Building REAL250005054364 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054364' /scratch/stefan/7922901/working/building/REAL250005054364 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054364 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054364/0 /scratch/stefan/7922901/working/building/REAL250005054364 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/501 `/scratch/stefan/7922901/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)COC(F)F)C(=O)C1=CC(=O)[N-]O1) `REAL250005054364.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054364 none CN(CCNC(=O)COC(F)F)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 12, 5, 15, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 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: [16, 6, 16, 23, 23, 48, 48, 48, 159, 199, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 23, 23, 23, 23, 48, 159, 159, 201, 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: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054364 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054364 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054364/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054364 Building REAL250005054365 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054365' /scratch/stefan/7922901/working/building/REAL250005054365 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054365 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054365/0 /scratch/stefan/7922901/working/building/REAL250005054365 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/502 `/scratch/stefan/7922901/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054365.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054365 none COC(C)(C)CC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 153, 153, 153, 90, 64, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 90, 90, 64, 64, 18, 18, 18, 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: 860 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054365 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054365 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054365/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054365 Building REAL250005054366 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054366' /scratch/stefan/7922901/working/building/REAL250005054366 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054366 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054366/0 /scratch/stefan/7922901/working/building/REAL250005054366 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/503 `/scratch/stefan/7922901/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054366.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054366 none CC(O)CCC(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 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, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 483 conformations in input total number of sets (complete confs): 483 using faster count positions algorithm for large data unique positions, atoms: [161, 154, 161, 158, 83, 83, 83, 71, 46, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 483, 161, 161, 158, 158, 83, 71, 71, 46, 46, 17, 17, 17, 1] 483 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: 1248 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054366 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054366 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054366/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054366 Building REAL250005054367 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054367' /scratch/stefan/7922901/working/building/REAL250005054367 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054367 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054367/0 /scratch/stefan/7922901/working/building/REAL250005054367 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/504 `/scratch/stefan/7922901/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054367.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054367 none C#CCC(C)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 144, 81, 144, 81, 81, 60, 42, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 172, 172, 172, 144, 144, 144, 144, 81, 60, 60, 42, 42, 16, 16, 16, 1] 172 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: 793 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054367 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054367 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054367/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054367 Building REAL250005054368 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054368' /scratch/stefan/7922901/working/building/REAL250005054368 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054368 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054368/0 /scratch/stefan/7922901/working/building/REAL250005054368 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/505 `/scratch/stefan/7922901/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCO)C(=O)NCCN(C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054368.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054368 none CC(CCO)C(=O)NCCN(C)C(=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.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 591 conformations in input total number of sets (complete confs): 591 using faster count positions algorithm for large data unique positions, atoms: [181, 117, 181, 197, 197, 117, 117, 75, 51, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 197, 197, 197, 197, 591, 117, 75, 75, 51, 51, 17, 17, 17, 1] 591 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: 1458 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054368 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054368 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054368/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054368 Building REAL250005054369 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054369' /scratch/stefan/7922901/working/building/REAL250005054369 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054369 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054369/0 /scratch/stefan/7922901/working/building/REAL250005054369 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/506 `/scratch/stefan/7922901/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C(F)=CC1CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054369.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054369 none CN(CCNC(=O)C(F)=CC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 36, 40, 73, 73, 73, 133, 133, 133, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 36, 36, 40, 40, 73, 133, 201, 201, 201, 201, 201, 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: 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: REAL250005054369 none CN(CCNC(=O)C(F)=CC1CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 137, 95, 39, 39, 8, 38, 8, 8, 1, 1, 1, 1, 164, 197, 197, 201, 201, 201, 201, 201, 164, 164, 164, 137, 137, 95, 95, 39, 8, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 789 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054369 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054369 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054369/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054369 Building REAL250005054370 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054370' /scratch/stefan/7922901/working/building/REAL250005054370 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054370 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054370/0 /scratch/stefan/7922901/working/building/REAL250005054370 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/507 `/scratch/stefan/7922901/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)CC1CC(F)C1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054370.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054370 none CN(CCNC(=O)CC1CC(F)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 18, 28, 31, 54, 54, 54, 175, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 28, 28, 31, 31, 54, 175, 175, 201, 201, 201, 201, 201, 201, 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: 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: REAL250005054370 none CN(CCNC(=O)CC1CC(F)C1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 155, 121, 37, 37, 7, 37, 1, 1, 1, 1, 1, 1, 176, 198, 198, 201, 201, 201, 201, 201, 176, 176, 176, 155, 155, 121, 121, 37, 7, 7, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37]) total number of confs: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054370 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054370 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054370/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054370 Building REAL250005054371 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054371' /scratch/stefan/7922901/working/building/REAL250005054371 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054371 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054371/0 /scratch/stefan/7922901/working/building/REAL250005054371 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/508 `/scratch/stefan/7922901/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@H](O)CF)C(=O)C1=CC(=O)[N-]O1) `REAL250005054371.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054371 none CN(CCNC(=O)[C@H](O)CF)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 324 conformations in input total number of sets (complete confs): 324 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 26, 26, 51, 51, 51, 106, 106, 106, 108, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 26, 26, 26, 26, 51, 318, 108, 108, 1] 324 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: 744 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054371 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054371 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054371/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054371 Building REAL250005054372 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054372' /scratch/stefan/7922901/working/building/REAL250005054372 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054372 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054372/0 /scratch/stefan/7922901/working/building/REAL250005054372 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/509 `/scratch/stefan/7922901/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=NN=CN1C)C(=O)C1=CC(=O)[N-]O1) `REAL250005054372.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054372 none CN(CCNC(=O)C1=NN=CN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 23, 25, 47, 47, 47, 69, 69, 69, 69, 69, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 23, 23, 25, 25, 47, 69, 69, 69, 69, 1] 69 rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 196 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054372 none CN(CCNC(=O)C1=NN=CN1C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [61, 55, 35, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 61, 69, 69, 69, 69, 69, 69, 69, 61, 61, 61, 55, 55, 35, 35, 9, 1, 2, 2, 2, 69] 69 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 301 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054372 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054372 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054372/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054372 Building REAL250005054373 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054373' /scratch/stefan/7922901/working/building/REAL250005054373 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054373 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054373/0 /scratch/stefan/7922901/working/building/REAL250005054373 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/510 `/scratch/stefan/7922901/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1(O)CC1)C(=O)C1=CC(=O)[N-]O1) `REAL250005054373.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054373 none CN(CCNC(=O)C1(O)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 570 conformations in input total number of sets (complete confs): 570 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 43, 47, 98, 98, 98, 190, 190, 190, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 43, 43, 47, 47, 98, 570, 190, 190, 190, 190, 1] 570 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: 1173 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: REAL250005054373 none CN(CCNC(=O)C1(O)CC1)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 570 conformations in input total number of sets (complete confs): 570 using faster count positions algorithm for large data unique positions, atoms: [143, 99, 67, 13, 13, 1, 13, 1, 1, 1, 1, 143, 183, 183, 190, 190, 190, 190, 190, 143, 143, 143, 99, 99, 67, 67, 13, 6, 1, 1, 1, 1, 190] 570 rigid atoms, others: [5, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32]) total number of confs: 739 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054373 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054373 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054373/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054373 Building REAL250005054374 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054374' /scratch/stefan/7922901/working/building/REAL250005054374 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054374 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054374/0 /scratch/stefan/7922901/working/building/REAL250005054374 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/511 `/scratch/stefan/7922901/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CC1) `REAL250005054374.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054374 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 29, 70, 103, 201, 201, 201, 201, 201, 201, 201, 201, 3, 15, 1, 1, 1, 1, 29, 29, 29, 70, 70, 103, 103, 201, 201, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 747 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: REAL250005054374 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 74, 129, 129, 143, 201, 201, 74, 74, 74, 34, 34, 18, 18, 4, 1, 143, 143, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 748 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054374 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054374 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054374/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054374 Building REAL250005054375 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054375' /scratch/stefan/7922901/working/building/REAL250005054375 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054375 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054375/0 /scratch/stefan/7922901/working/building/REAL250005054375 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/512 `/scratch/stefan/7922901/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)F) `REAL250005054375.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054375 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [95, 46, 28, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 95, 149, 149, 195, 195, 195, 95, 95, 95, 46, 46, 28, 28, 9, 1, 195, 195, 195, 195, 195, 195] 195 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 793 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054375 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054375 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054375/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054375 Building REAL250005054376 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054376' /scratch/stefan/7922901/working/building/REAL250005054376 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054376 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054376/0 /scratch/stefan/7922901/working/building/REAL250005054376 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/513 `/scratch/stefan/7922901/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(F)F) `REAL250005054376.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054376 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(F)F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [85, 47, 26, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 85, 93, 93, 93, 93, 93, 85, 85, 85, 47, 47, 26, 26, 7, 1, 93, 93, 93] 93 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 364 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054376 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054376 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054376/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054376 Building REAL250005054377 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054377' /scratch/stefan/7922901/working/building/REAL250005054377 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054377 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054377/0 /scratch/stefan/7922901/working/building/REAL250005054377 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/514 `/scratch/stefan/7922901/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054377.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054377 none COCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 129, 95, 129, 44, 95, 26, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 195, 95, 95, 95, 44, 44, 26, 26, 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: 795 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054377 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054377 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054377/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054377 Building REAL250005054378 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054378' /scratch/stefan/7922901/working/building/REAL250005054378 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054378 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054378/0 /scratch/stefan/7922901/working/building/REAL250005054378 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/515 `/scratch/stefan/7922901/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CC=N1) `REAL250005054378.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054378 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 19, 61, 91, 186, 186, 186, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 61, 61, 91, 91, 186, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 677 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054378 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 62, 40, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 120, 191, 191, 201, 201, 201, 201, 201, 120, 120, 120, 62, 62, 40, 40, 11, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 675 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054378 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054378 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054378/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054378 Building REAL250005054379 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054379' /scratch/stefan/7922901/working/building/REAL250005054379 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054379 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054379/0 /scratch/stefan/7922901/working/building/REAL250005054379 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/516 `/scratch/stefan/7922901/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NC=C1) `REAL250005054379.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054379 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 36, 60, 120, 120, 120, 128, 128, 128, 128, 128, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 36, 36, 60, 60, 120, 128, 1, 1, 1, 1] 128 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 459 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: REAL250005054379 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [75, 40, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 75, 128, 128, 128, 128, 128, 128, 128, 75, 75, 75, 40, 40, 28, 28, 7, 1, 128, 128, 128, 128] 128 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 441 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054379 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054379 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054379/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054379 Building REAL250005054380 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054380' /scratch/stefan/7922901/working/building/REAL250005054380 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054380 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054380/0 /scratch/stefan/7922901/working/building/REAL250005054380 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/517 `/scratch/stefan/7922901/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054380.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054380 none CCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [132, 130, 69, 53, 69, 33, 53, 24, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 131, 131, 53, 53, 53, 33, 33, 24, 24, 8, 1] 133 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: 541 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054380 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054380 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054380/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054380 Building REAL250005054381 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054381' /scratch/stefan/7922901/working/building/REAL250005054381 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054381 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054381/0 /scratch/stefan/7922901/working/building/REAL250005054381 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/518 `/scratch/stefan/7922901/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CN=C1) `REAL250005054381.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054381 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [19, 11, 19, 61, 105, 198, 200, 198, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 19, 19, 19, 61, 61, 105, 105, 200, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 773 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: REAL250005054381 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [76, 42, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 76, 138, 138, 201, 201, 201, 199, 201, 76, 76, 76, 42, 42, 26, 26, 6, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 599 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054381 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054381 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054381/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054381 Building REAL250005054382 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054382' /scratch/stefan/7922901/working/building/REAL250005054382 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054382 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054382/0 /scratch/stefan/7922901/working/building/REAL250005054382 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/519 `/scratch/stefan/7922901/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CO1) `REAL250005054382.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054382 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 12, 27, 73, 107, 197, 197, 197, 201, 201, 201, 201, 201, 1, 12, 1, 1, 1, 1, 1, 27, 27, 27, 73, 73, 107, 107, 197, 201, 1, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 735 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054382 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 50, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 99, 185, 185, 201, 201, 201, 201, 101, 101, 101, 50, 50, 30, 30, 9, 1, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 665 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054382 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054382 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054382/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054382 Building REAL250005054383 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054383' /scratch/stefan/7922901/working/building/REAL250005054383 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054383 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054383/0 /scratch/stefan/7922901/working/building/REAL250005054383 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/520 `/scratch/stefan/7922901/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054383.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054383 none CC(=O)NCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 120, 71, 65, 71, 33, 65, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 120, 120, 65, 65, 65, 33, 33, 18, 18, 4, 1] 132 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: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054383 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054383 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054383/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054383 Building REAL250005054384 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054384' /scratch/stefan/7922901/working/building/REAL250005054384 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054384 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054384/0 /scratch/stefan/7922901/working/building/REAL250005054384 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/521 `/scratch/stefan/7922901/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CC=C1) `REAL250005054384.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054384 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 11, 31, 53, 107, 107, 107, 117, 117, 117, 117, 117, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 31, 31, 53, 53, 107, 117, 1, 1, 1, 1, 1] 117 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 411 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: REAL250005054384 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 42, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 117, 117, 117, 117, 117, 117, 117, 71, 71, 71, 42, 42, 26, 26, 9, 1, 117, 117, 117, 117, 117] 117 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 415 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054384 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054384 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054384/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054384 Building REAL250005054385 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054385' /scratch/stefan/7922901/working/building/REAL250005054385 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054385 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054385/0 /scratch/stefan/7922901/working/building/REAL250005054385 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/522 `/scratch/stefan/7922901/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054385.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054385 none CC(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 82, 62, 82, 35, 62, 22, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 112, 112, 112, 112, 62, 62, 62, 35, 35, 22, 22, 8, 1] 112 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: 475 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054385 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054385 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054385/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054385 Building REAL250005054386 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054386' /scratch/stefan/7922901/working/building/REAL250005054386 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054386 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054386/0 /scratch/stefan/7922901/working/building/REAL250005054386 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/523 `/scratch/stefan/7922901/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCCC1) `REAL250005054386.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054386 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 53, 93, 195, 195, 195, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 53, 53, 93, 93, 195, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 747 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054386 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 41, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 81, 153, 153, 201, 201, 201, 201, 201, 81, 81, 81, 41, 41, 22, 22, 5, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 704 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054386 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054386 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054386/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054386 Building REAL250005054387 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054387' /scratch/stefan/7922901/working/building/REAL250005054387 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054387 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054387/0 /scratch/stefan/7922901/working/building/REAL250005054387 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/524 `/scratch/stefan/7922901/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CC=N1) `REAL250005054387.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054387 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 19, 57, 87, 171, 171, 171, 181, 181, 181, 181, 181, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 57, 57, 87, 87, 171, 181, 1, 1, 1] 181 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 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]) 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: REAL250005054387 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [97, 48, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 97, 171, 171, 181, 181, 181, 181, 181, 97, 97, 97, 48, 48, 30, 30, 9, 1, 181, 181, 181] 181 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054387 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054387 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054387/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054387 Building REAL250005054388 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054388' /scratch/stefan/7922901/working/building/REAL250005054388 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054388 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054388/0 /scratch/stefan/7922901/working/building/REAL250005054388 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/525 `/scratch/stefan/7922901/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CCCC1) `REAL250005054388.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054388 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 35, 72, 95, 201, 201, 201, 201, 201, 201, 201, 201, 5, 15, 1, 1, 1, 1, 1, 1, 35, 35, 35, 72, 72, 95, 95, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL250005054388 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 54, 105, 105, 121, 201, 201, 201, 201, 54, 54, 54, 24, 24, 16, 16, 4, 1, 121, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054388 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054388 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054388/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054388 Building REAL250005054389 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054389' /scratch/stefan/7922901/working/building/REAL250005054389 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054389 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054389/0 /scratch/stefan/7922901/working/building/REAL250005054389 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/526 `/scratch/stefan/7922901/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CS1) `REAL250005054389.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054389 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 22, 72, 111, 200, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 22, 22, 22, 72, 72, 111, 111, 201, 201, 1, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 780 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054389 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 77, 153, 153, 201, 201, 201, 201, 77, 77, 77, 38, 38, 22, 22, 4, 1, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 605 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054389 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054389 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054389/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054389 Building REAL250005054390 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054390' /scratch/stefan/7922901/working/building/REAL250005054390 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054390 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054390/0 /scratch/stefan/7922901/working/building/REAL250005054390 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/527 `/scratch/stefan/7922901/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054390.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054390 none CC1CC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 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, 87, 56, 87, 32, 56, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 123, 123, 56, 56, 56, 32, 32, 20, 20, 6, 1] 123 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: 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: REAL250005054390 none CC1CC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 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 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, 8, 8, 18, 18, 41, 57, 119, 119, 119, 123, 123, 123, 123, 123, 2, 2, 2, 1, 1, 1, 1, 18, 18, 18, 41, 41, 57, 57, 119, 123] 123 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: 436 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054390 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054390 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054390/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054390 Building REAL250005054391 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054391' /scratch/stefan/7922901/working/building/REAL250005054391 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054391 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054391/0 /scratch/stefan/7922901/working/building/REAL250005054391 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/528 `/scratch/stefan/7922901/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054391.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054391 none CCOCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [150, 149, 98, 69, 63, 69, 39, 63, 24, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 98, 98, 63, 63, 63, 39, 39, 24, 24, 7, 1] 150 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: 524 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054391 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054391 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054391/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054391 Building REAL250005054392 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054392' /scratch/stefan/7922901/working/building/REAL250005054392 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054392 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054392/0 /scratch/stefan/7922901/working/building/REAL250005054392 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/529 `/scratch/stefan/7922901/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054392.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054392 none CC(C)=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 90, 63, 90, 41, 63, 26, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126, 63, 63, 63, 41, 41, 26, 26, 8, 1] 126 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: 497 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054392 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054392 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054392/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054392 Building REAL250005054393 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054393' /scratch/stefan/7922901/working/building/REAL250005054393 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054393 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054393/0 /scratch/stefan/7922901/working/building/REAL250005054393 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/530 `/scratch/stefan/7922901/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COCCO1) `REAL250005054393.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054393 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 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: [29, 9, 29, 84, 112, 198, 199, 198, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 84, 84, 112, 112, 199, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 756 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054393 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 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: [75, 41, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 75, 150, 150, 201, 201, 201, 201, 201, 75, 75, 75, 41, 41, 26, 26, 7, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054393 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054393 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054393/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054393 Building REAL250005054394 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054394' /scratch/stefan/7922901/working/building/REAL250005054394 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054394 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054394/0 /scratch/stefan/7922901/working/building/REAL250005054394 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/531 `/scratch/stefan/7922901/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054394.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054394 none CC(=O)NC(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 100, 74, 100, 66, 74, 34, 66, 20, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 100, 100, 100, 100, 66, 66, 66, 34, 34, 20, 20, 5, 1] 101 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: 416 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054394 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054394 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054394/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054394 Building REAL250005054395 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054395' /scratch/stefan/7922901/working/building/REAL250005054395 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054395 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054395/0 /scratch/stefan/7922901/working/building/REAL250005054395 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/532 `/scratch/stefan/7922901/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005054395.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054395 none CC1=CC=C(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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 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, 113, 67, 113, 41, 67, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 141, 67, 67, 67, 41, 41, 26, 26, 7, 1] 141 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: 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: REAL250005054395 none CC1=CC=C(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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 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, 22, 22, 61, 83, 137, 137, 137, 141, 141, 141, 141, 141, 1, 2, 2, 2, 1, 1, 22, 22, 22, 61, 61, 83, 83, 137, 141] 141 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: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054395 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054395 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054395/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054395 Building REAL250005054396 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054396' /scratch/stefan/7922901/working/building/REAL250005054396 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054396 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054396/0 /scratch/stefan/7922901/working/building/REAL250005054396 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/533 `/scratch/stefan/7922901/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCO1) `REAL250005054396.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054396 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 19, 52, 83, 151, 151, 151, 166, 166, 166, 166, 166, 1, 7, 1, 1, 1, 1, 1, 19, 19, 19, 52, 52, 83, 83, 151, 166, 1, 1, 1, 1, 1, 1, 1] 166 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 595 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: REAL250005054396 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [94, 52, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 93, 153, 153, 166, 166, 166, 166, 94, 94, 94, 52, 52, 35, 35, 11, 1, 166, 166, 166, 166, 166, 166, 166] 166 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 572 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054396 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054396 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054396/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054396 Building REAL250005054397 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054397' /scratch/stefan/7922901/working/building/REAL250005054397 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054397 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054397/0 /scratch/stefan/7922901/working/building/REAL250005054397 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/534 `/scratch/stefan/7922901/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054397.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054397 none CSCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 112, 82, 112, 43, 82, 25, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 175, 175, 82, 82, 82, 43, 43, 25, 25, 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: 791 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054397 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054397 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054397/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054397 Building REAL250005054398 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054398' /scratch/stefan/7922901/working/building/REAL250005054398 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054398 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054398/0 /scratch/stefan/7922901/working/building/REAL250005054398 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/535 `/scratch/stefan/7922901/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=NO1) `REAL250005054398.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054398 none CC1=CC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 171, 97, 171, 51, 97, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 194, 97, 97, 97, 51, 51, 31, 31, 9, 1] 194 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: 614 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054398 none CC1=CC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 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, 10, 10, 28, 28, 80, 122, 190, 190, 190, 194, 194, 194, 194, 194, 1, 1, 2, 2, 2, 1, 28, 28, 28, 80, 80, 122, 122, 190, 194] 194 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: 761 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054398 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054398 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054398/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054398 Building REAL250005054399 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054399' /scratch/stefan/7922901/working/building/REAL250005054399 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054399 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054399/0 /scratch/stefan/7922901/working/building/REAL250005054399 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/536 `/scratch/stefan/7922901/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054399.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054399 none CSCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 75, 75, 57, 45, 57, 25, 45, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 135, 135, 135, 75, 75, 75, 75, 45, 45, 45, 25, 25, 16, 16, 4, 1] 135 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: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054399 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054399 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054399/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054399 Building REAL250005054400 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054400' /scratch/stefan/7922901/working/building/REAL250005054400 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054400 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054400/0 /scratch/stefan/7922901/working/building/REAL250005054400 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/537 `/scratch/stefan/7922901/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054400.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054400 none CC(C)CCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 180, 193, 169, 99, 65, 99, 31, 65, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 193, 193, 181, 181, 170, 170, 65, 65, 65, 31, 31, 17, 17, 4, 1] 193 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: 833 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054400 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054400 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054400/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054400 Building REAL250005054401 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054401' /scratch/stefan/7922901/working/building/REAL250005054401 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054401 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054401/0 /scratch/stefan/7922901/working/building/REAL250005054401 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/538 `/scratch/stefan/7922901/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CSC=C1) `REAL250005054401.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054401 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CSC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 30, 80, 118, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 30, 30, 30, 80, 80, 118, 118, 201, 201, 1, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 787 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: REAL250005054401 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CSC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 70, 139, 139, 201, 201, 201, 201, 70, 70, 70, 35, 35, 18, 18, 4, 1, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 591 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054401 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054401 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054401/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054401 Building REAL250005054402 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054402' /scratch/stefan/7922901/working/building/REAL250005054402 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054402 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054402/0 /scratch/stefan/7922901/working/building/REAL250005054402 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/539 `/scratch/stefan/7922901/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C=CO1) `REAL250005054402.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054402 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 201, 143, 78, 143, 45, 78, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 78, 78, 78, 45, 45, 27, 27, 9, 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: 599 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054402 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [1, 1, 1, 1, 9, 9, 25, 25, 69, 103, 197, 197, 197, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 25, 25, 25, 69, 69, 103, 103, 197, 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: 753 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054402 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054402 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054402/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054402 Building REAL250005054403 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054403' /scratch/stefan/7922901/working/building/REAL250005054403 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054403 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054403/0 /scratch/stefan/7922901/working/building/REAL250005054403 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/540 `/scratch/stefan/7922901/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1C=CCC1) `REAL250005054403.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054403 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1C=CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 30, 70, 99, 201, 201, 201, 201, 201, 201, 201, 201, 5, 14, 1, 1, 1, 1, 1, 1, 30, 30, 30, 70, 70, 99, 99, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 732 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: REAL250005054403 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1C=CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 62, 126, 126, 134, 201, 201, 201, 201, 62, 62, 62, 31, 31, 18, 18, 4, 1, 134, 134, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 736 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054403 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054403 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054403/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054403 Building REAL250005054404 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054404' /scratch/stefan/7922901/working/building/REAL250005054404 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054404 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054404/0 /scratch/stefan/7922901/working/building/REAL250005054404 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/541 `/scratch/stefan/7922901/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=NN=N1) `REAL250005054404.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054404 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=NN=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 80, 124, 155, 201, 201, 201, 201, 201, 201, 201, 201, 9, 41, 1, 1, 1, 1, 1, 1, 80, 80, 80, 124, 124, 155, 155, 201, 201, 9, 9, 1] 201 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 772 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: REAL250005054404 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=NN=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 105, 105, 161, 201, 201, 201, 201, 65, 65, 65, 34, 34, 18, 18, 4, 1, 161, 161, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 713 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054404 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054404 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054404/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054404 Building REAL250005054405 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054405' /scratch/stefan/7922901/working/building/REAL250005054405 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054405 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054405/0 /scratch/stefan/7922901/working/building/REAL250005054405 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/542 `/scratch/stefan/7922901/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN(C)N=C1) `REAL250005054405.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054405 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 27, 74, 108, 195, 195, 195, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 27, 27, 27, 74, 74, 108, 108, 195, 201, 1, 2, 2, 2, 1] 201 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 767 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: REAL250005054405 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 84, 155, 155, 201, 201, 201, 201, 201, 84, 84, 84, 43, 43, 28, 28, 8, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 611 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054405 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054405 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054405/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054405 Building REAL250005054406 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054406' /scratch/stefan/7922901/working/building/REAL250005054406 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054406 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054406/0 /scratch/stefan/7922901/working/building/REAL250005054406 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/543 `/scratch/stefan/7922901/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC=CCC1) `REAL250005054406.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054406 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC=CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 55, 98, 198, 198, 198, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 55, 55, 98, 98, 198, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 759 number of broken/clashed sets: 100 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054406 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC=CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 68, 152, 153, 201, 201, 201, 201, 201, 69, 69, 69, 35, 35, 22, 22, 5, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 692 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054406 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054406 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054406/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054406 Building REAL250005054407 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054407' /scratch/stefan/7922901/working/building/REAL250005054407 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054407 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054407/0 /scratch/stefan/7922901/working/building/REAL250005054407 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/544 `/scratch/stefan/7922901/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005054407.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054407 none CC1=NOC(C(=O)N(C)CCNC(=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', '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, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 149, 137, 89, 137, 48, 89, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 89, 89, 89, 48, 48, 30, 30, 7, 1, 149] 149 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: 489 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054407 none CC1=NOC(C(=O)N(C)CCNC(=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', '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, 1, 8, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 22, 22, 55, 83, 145, 145, 145, 149, 149, 149, 149, 149, 1, 2, 2, 2, 22, 22, 22, 55, 55, 83, 83, 145, 149, 1] 149 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: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054407 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054407 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054407/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054407 Building REAL250005054408 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054408' /scratch/stefan/7922901/working/building/REAL250005054408 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054408 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054408/0 /scratch/stefan/7922901/working/building/REAL250005054408 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/545 `/scratch/stefan/7922901/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CN1) `REAL250005054408.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054408 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 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: [23, 11, 23, 75, 105, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 23, 23, 23, 75, 75, 105, 105, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 744 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: REAL250005054408 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 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: [82, 40, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 82, 157, 157, 201, 201, 201, 201, 82, 82, 82, 40, 40, 24, 24, 6, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 603 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054408 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054408 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054408/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054408 Building REAL250005054409 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054409' /scratch/stefan/7922901/working/building/REAL250005054409 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054409 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054409/0 /scratch/stefan/7922901/working/building/REAL250005054409 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/546 `/scratch/stefan/7922901/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054409.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054409 none CC(=O)CCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 129, 201, 78, 63, 24, 24, 24, 18, 24, 11, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 125, 125, 90, 90, 64, 64, 24, 24, 24, 18, 18, 11, 11, 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: 905 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054409 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054409 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054409/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054409 Building REAL250005054410 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054410' /scratch/stefan/7922901/working/building/REAL250005054410 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054410 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054410/0 /scratch/stefan/7922901/working/building/REAL250005054410 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/547 `/scratch/stefan/7922901/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COC=C1) `REAL250005054410.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054410 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [27, 11, 27, 66, 93, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 27, 27, 27, 66, 66, 93, 93, 201, 201, 1, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 730 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: REAL250005054410 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [70, 34, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 70, 126, 126, 201, 201, 201, 201, 70, 70, 70, 34, 34, 20, 20, 4, 1, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 569 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054410 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054410 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054410/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054410 Building REAL250005054411 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054411' /scratch/stefan/7922901/working/building/REAL250005054411 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054411 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054411/0 /scratch/stefan/7922901/working/building/REAL250005054411 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/548 `/scratch/stefan/7922901/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=CC=N1) `REAL250005054411.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054411 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=CC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 45, 81, 112, 201, 201, 201, 201, 201, 201, 201, 201, 8, 27, 1, 1, 1, 1, 1, 1, 45, 45, 45, 81, 81, 112, 112, 201, 201, 8, 8, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 787 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054411 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=CC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 58, 103, 103, 169, 201, 201, 201, 201, 58, 58, 58, 31, 31, 16, 16, 4, 1, 169, 169, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 725 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054411 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054411 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054411/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054411 Building REAL250005054412 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054412' /scratch/stefan/7922901/working/building/REAL250005054412 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054412 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054412/0 /scratch/stefan/7922901/working/building/REAL250005054412 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/549 `/scratch/stefan/7922901/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)OC=C1) `REAL250005054412.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054412 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 143, 81, 143, 38, 81, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 81, 81, 81, 38, 38, 24, 24, 7, 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: 585 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054412 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 8, 8, 24, 24, 81, 111, 197, 197, 197, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 24, 24, 24, 81, 81, 111, 111, 197, 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: 743 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054412 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054412 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054412/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054412 Building REAL250005054413 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054413' /scratch/stefan/7922901/working/building/REAL250005054413 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054413 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054413/0 /scratch/stefan/7922901/working/building/REAL250005054413 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/550 `/scratch/stefan/7922901/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054413.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054413 none CCCCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 179, 144, 130, 59, 57, 59, 39, 57, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 181, 181, 147, 147, 131, 131, 57, 57, 57, 39, 39, 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: 955 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054413 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054413 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054413/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054413 Building REAL250005054414 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054414' /scratch/stefan/7922901/working/building/REAL250005054414 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054414 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054414/0 /scratch/stefan/7922901/working/building/REAL250005054414 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/551 `/scratch/stefan/7922901/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(C)(C)C) `REAL250005054414.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054414 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(C)(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [86, 41, 26, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 86, 154, 154, 177, 180, 179, 180, 86, 86, 86, 41, 41, 26, 26, 9, 1, 178, 178, 180, 180, 180, 180, 180, 180, 180, 180, 180] 180 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 683 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054414 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054414 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054414/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054414 Building REAL250005054415 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054415' /scratch/stefan/7922901/working/building/REAL250005054415 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054415 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054415/0 /scratch/stefan/7922901/working/building/REAL250005054415 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/552 `/scratch/stefan/7922901/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CN1C) `REAL250005054415.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054415 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CN1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 23, 69, 99, 201, 201, 201, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 69, 69, 99, 99, 201, 201, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 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, 33, 34, 35]) total number of confs: 747 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: REAL250005054415 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CN1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 42, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 81, 169, 169, 201, 201, 201, 201, 201, 81, 81, 81, 42, 42, 24, 24, 4, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 603 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054415 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054415 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054415/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054415 Building REAL250005054416 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054416' /scratch/stefan/7922901/working/building/REAL250005054416 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054416 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054416/0 /scratch/stefan/7922901/working/building/REAL250005054416 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/553 `/scratch/stefan/7922901/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054416.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054416 none CCCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [200, 169, 167, 83, 67, 83, 34, 67, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 170, 170, 168, 168, 67, 67, 67, 34, 34, 18, 18, 4, 1] 200 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: 860 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054416 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054416 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054416/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054416 Building REAL250005054417 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054417' /scratch/stefan/7922901/working/building/REAL250005054417 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054417 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054417/0 /scratch/stefan/7922901/working/building/REAL250005054417 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/554 `/scratch/stefan/7922901/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054417.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054417 none CC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 55, 71, 35, 55, 26, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 71, 55, 55, 55, 35, 35, 26, 26, 7, 1] 71 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: 260 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054417 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054417 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054417/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054417 Building REAL250005054418 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054418' /scratch/stefan/7922901/working/building/REAL250005054418 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054418 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054418/0 /scratch/stefan/7922901/working/building/REAL250005054418 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/555 `/scratch/stefan/7922901/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054418.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054418 none CCC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 86, 68, 86, 55, 68, 35, 55, 25, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 86, 86, 86, 86, 55, 55, 55, 35, 35, 25, 25, 8, 1] 96 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: 415 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054418 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054418 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054418/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054418 Building REAL250005054419 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054419' /scratch/stefan/7922901/working/building/REAL250005054419 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054419 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054419/0 /scratch/stefan/7922901/working/building/REAL250005054419 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/556 `/scratch/stefan/7922901/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CSCC#N) `REAL250005054419.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054419 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CSCC#N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 48, 64, 64, 72, 153, 201, 201, 48, 48, 48, 26, 26, 14, 14, 4, 1, 72, 72, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 664 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054419 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054419 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054419/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054419 Building REAL250005054420 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054420' /scratch/stefan/7922901/working/building/REAL250005054420 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054420 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054420/0 /scratch/stefan/7922901/working/building/REAL250005054420 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/557 `/scratch/stefan/7922901/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054420.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054420 none CC(=O)N(C)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 21, 15, 13, 15, 12, 13, 8, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 19, 19, 13, 13, 13, 12, 12, 8, 8, 3, 1] 21 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054420 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054420 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054420/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054420 Building REAL250005054421 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054421' /scratch/stefan/7922901/working/building/REAL250005054421 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054421 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054421/0 /scratch/stefan/7922901/working/building/REAL250005054421 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/558 `/scratch/stefan/7922901/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054421.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054421 none CCC(CC)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [95, 91, 73, 91, 95, 63, 73, 33, 63, 20, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 91, 96, 96, 96, 96, 96, 63, 63, 63, 33, 33, 20, 20, 6, 1] 99 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: 442 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054421 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054421 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054421/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054421 Building REAL250005054422 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054422' /scratch/stefan/7922901/working/building/REAL250005054422 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054422 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054422/0 /scratch/stefan/7922901/working/building/REAL250005054422 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/559 `/scratch/stefan/7922901/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054422.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054422 none CC(C)OCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 120, 90, 46, 40, 46, 25, 40, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 120, 120, 90, 90, 40, 40, 40, 25, 25, 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: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054422 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054422 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054422/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054422 Building REAL250005054423 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054423' /scratch/stefan/7922901/working/building/REAL250005054423 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054423 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054423/0 /scratch/stefan/7922901/working/building/REAL250005054423 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/560 `/scratch/stefan/7922901/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1COCCO1) `REAL250005054423.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054423 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1COCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 15, 41, 63, 124, 124, 124, 129, 129, 129, 129, 129, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 41, 41, 63, 63, 124, 129, 1, 1, 1, 1, 1, 1, 1] 129 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 455 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: REAL250005054423 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1COCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [79, 41, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 79, 123, 123, 129, 129, 129, 129, 129, 79, 79, 79, 41, 41, 27, 27, 8, 1, 129, 129, 129, 129, 129, 129, 129] 129 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 439 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054423 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054423 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054423/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054423 Building REAL250005054424 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054424' /scratch/stefan/7922901/working/building/REAL250005054424 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054424 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054424/0 /scratch/stefan/7922901/working/building/REAL250005054424 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/561 `/scratch/stefan/7922901/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NNC=C1) `REAL250005054424.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054424 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NNC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 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: [30, 12, 30, 69, 105, 183, 183, 183, 201, 201, 201, 201, 201, 1, 12, 1, 1, 1, 1, 1, 30, 30, 30, 69, 69, 105, 105, 183, 201, 1, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 700 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054424 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NNC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 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: [108, 54, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 108, 193, 193, 201, 201, 201, 201, 108, 108, 108, 54, 54, 36, 36, 11, 1, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054424 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054424/1 /scratch/stefan/7922901/working/building/REAL250005054424 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/562 `/scratch/stefan/7922901/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NN1) `REAL250005054424.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054424 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 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: [24, 11, 24, 74, 108, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 24, 24, 24, 74, 74, 108, 108, 201, 201, 1, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 770 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: REAL250005054424 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 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: [73, 35, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 73, 142, 142, 201, 201, 201, 201, 73, 73, 73, 35, 35, 22, 22, 4, 1, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 579 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054424 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054424 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054424/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054424/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054424 Building REAL250005054425 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054425' /scratch/stefan/7922901/working/building/REAL250005054425 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054425 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054425/0 /scratch/stefan/7922901/working/building/REAL250005054425 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/563 `/scratch/stefan/7922901/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054425.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054425 none CSC(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 92, 83, 92, 66, 83, 39, 66, 25, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 120, 120, 120, 92, 92, 92, 92, 66, 66, 66, 39, 39, 25, 25, 6, 1] 120 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: 407 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054425 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054425 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054425/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054425 Building REAL250005054426 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054426' /scratch/stefan/7922901/working/building/REAL250005054426 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054426 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054426/0 /scratch/stefan/7922901/working/building/REAL250005054426 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/564 `/scratch/stefan/7922901/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054426.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054426 none CCOC(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 76, 72, 76, 57, 72, 35, 57, 23, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 76, 76, 76, 76, 57, 57, 57, 35, 35, 23, 23, 8, 1] 82 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: 304 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054426 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054426 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054426/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054426 Building REAL250005054427 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054427' /scratch/stefan/7922901/working/building/REAL250005054427 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054427 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054427/0 /scratch/stefan/7922901/working/building/REAL250005054427 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/565 `/scratch/stefan/7922901/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054427.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054427 none CCOCCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 96, 90, 25, 21, 25, 19, 21, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 175, 175, 113, 113, 91, 91, 21, 21, 21, 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: 925 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054427 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054427 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054427/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054427 Building REAL250005054428 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054428' /scratch/stefan/7922901/working/building/REAL250005054428 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054428 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054428/0 /scratch/stefan/7922901/working/building/REAL250005054428 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/566 `/scratch/stefan/7922901/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)COCC1CC1) `REAL250005054428.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054428 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)COCC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 80, 107, 157, 180, 201, 201, 201, 201, 201, 201, 201, 201, 52, 80, 24, 9, 1, 1, 1, 1, 107, 107, 107, 157, 157, 180, 180, 201, 201, 52, 52, 9, 9, 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: 842 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054428 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)COCC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 27, 33, 33, 45, 91, 136, 201, 201, 27, 27, 27, 18, 18, 9, 9, 3, 1, 45, 45, 136, 136, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054428 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054428 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054428/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054428 Building REAL250005054429 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054429' /scratch/stefan/7922901/working/building/REAL250005054429 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054429 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054429/0 /scratch/stefan/7922901/working/building/REAL250005054429 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/567 `/scratch/stefan/7922901/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CCCO1) `REAL250005054429.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054429 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [28, 16, 28, 66, 88, 165, 165, 165, 166, 166, 166, 166, 166, 5, 16, 1, 1, 1, 1, 1, 1, 28, 28, 28, 66, 66, 88, 88, 165, 166, 5, 5, 1, 1, 1, 1, 1, 1, 1] 166 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 615 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: REAL250005054429 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [59, 28, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 59, 125, 125, 134, 166, 166, 166, 166, 59, 59, 59, 28, 28, 19, 19, 5, 1, 134, 134, 166, 166, 166, 166, 166, 166, 166] 166 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 583 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054429 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054429 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054429/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054429 Building REAL250005054430 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054430' /scratch/stefan/7922901/working/building/REAL250005054430 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054430 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054430/0 /scratch/stefan/7922901/working/building/REAL250005054430 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/568 `/scratch/stefan/7922901/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNN=C1) `REAL250005054430.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054430 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNN=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 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: [23, 11, 23, 53, 65, 133, 133, 133, 141, 141, 141, 141, 141, 1, 11, 1, 1, 1, 1, 1, 23, 23, 23, 53, 53, 65, 65, 133, 141, 1, 1, 1] 141 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 479 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054430 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNN=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 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: [94, 47, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 94, 165, 165, 165, 165, 165, 165, 94, 94, 94, 47, 47, 29, 29, 9, 1, 165, 165, 165] 165 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 552 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054430 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054430 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054430/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054430 Building REAL250005054431 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054431' /scratch/stefan/7922901/working/building/REAL250005054431 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054431 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054431/0 /scratch/stefan/7922901/working/building/REAL250005054431 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/569 `/scratch/stefan/7922901/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054431.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054431 none COCCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 73, 55, 25, 23, 25, 21, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 107, 107, 107, 104, 104, 79, 79, 55, 55, 23, 23, 23, 21, 21, 14, 14, 4, 1] 107 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: 518 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054431 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054431 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054431/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054431 Building REAL250005054432 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054432' /scratch/stefan/7922901/working/building/REAL250005054432 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054432 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054432/0 /scratch/stefan/7922901/working/building/REAL250005054432 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/570 `/scratch/stefan/7922901/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054432.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054432 none CCOC1CC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 139, 139, 139, 79, 52, 79, 30, 52, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 139, 139, 139, 139, 52, 52, 52, 30, 30, 19, 19, 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: 612 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: REAL250005054432 none CCOC1CC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 8, 8, 25, 25, 52, 68, 127, 127, 127, 139, 139, 139, 139, 139, 12, 12, 12, 12, 12, 1, 1, 1, 1, 25, 25, 25, 52, 52, 68, 68, 127, 139] 201 rigid atoms, others: [2, 3, 4, 5, 6, 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, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 515 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054432 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054432 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054432/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054432 Building REAL250005054433 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054433' /scratch/stefan/7922901/working/building/REAL250005054433 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054433 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054433/0 /scratch/stefan/7922901/working/building/REAL250005054433 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/571 `/scratch/stefan/7922901/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NSN=C1) `REAL250005054433.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054433 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NSN=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 60, 96, 187, 187, 187, 192, 192, 192, 192, 192, 1, 10, 1, 1, 1, 1, 1, 21, 21, 21, 60, 60, 96, 96, 187, 192, 1] 192 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 709 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054433 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NSN=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [98, 53, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 98, 180, 180, 192, 192, 192, 192, 98, 98, 98, 53, 53, 30, 30, 7, 1, 192] 192 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29]) total number of confs: 647 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054433 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054433 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054433/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054433 Building REAL250005054434 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054434' /scratch/stefan/7922901/working/building/REAL250005054434 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054434 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054434/0 /scratch/stefan/7922901/working/building/REAL250005054434 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/572 `/scratch/stefan/7922901/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=NS1) `REAL250005054434.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054434 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=NS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 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: [25, 11, 25, 67, 99, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 25, 25, 25, 67, 67, 99, 99, 201, 201, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005054434 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=NS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 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: [69, 34, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 69, 135, 135, 201, 201, 201, 201, 69, 69, 69, 34, 34, 20, 20, 4, 1, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29]) total number of confs: 582 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054434 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054434 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054434/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054434 Building REAL250005054435 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054435' /scratch/stefan/7922901/working/building/REAL250005054435 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054435 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054435/0 /scratch/stefan/7922901/working/building/REAL250005054435 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/573 `/scratch/stefan/7922901/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NOC=C1) `REAL250005054435.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054435 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NOC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 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: [27, 12, 27, 72, 107, 184, 184, 184, 196, 196, 196, 196, 196, 1, 12, 1, 1, 1, 1, 1, 27, 27, 27, 72, 72, 107, 107, 184, 196, 1, 1] 196 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005054435 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NOC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 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: [110, 52, 33, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 110, 180, 180, 196, 196, 196, 196, 110, 110, 110, 52, 52, 33, 33, 11, 1, 196, 196] 196 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 647 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054435 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054435 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054435/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054435 Building REAL250005054436 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054436' /scratch/stefan/7922901/working/building/REAL250005054436 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054436 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054436/0 /scratch/stefan/7922901/working/building/REAL250005054436 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/574 `/scratch/stefan/7922901/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005054436.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054436 none CC(=CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 22, 22, 48, 48, 99, 122, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 7, 7, 7, 7, 48, 48, 48, 99, 99, 122, 122, 201, 201, 1, 1, 1, 1, 1] 201 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: 756 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: REAL250005054436 none CC(=CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 86, 61, 86, 34, 61, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 146, 201, 201, 146, 146, 146, 146, 61, 61, 61, 34, 34, 20, 20, 5, 1, 201, 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, 38]) total number of confs: 736 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054436 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054436 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054436/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054436 Building REAL250005054437 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054437' /scratch/stefan/7922901/working/building/REAL250005054437 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054437 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054437/0 /scratch/stefan/7922901/working/building/REAL250005054437 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/575 `/scratch/stefan/7922901/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005054437.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054437 none CC1=NNC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 139, 79, 139, 38, 79, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 79, 79, 79, 38, 38, 23, 23, 5, 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: 578 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: REAL250005054437 none CC1=NNC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 28, 28, 71, 100, 200, 200, 200, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 28, 28, 28, 71, 71, 100, 100, 200, 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: 716 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054437 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054437/1 /scratch/stefan/7922901/working/building/REAL250005054437 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/576 `/scratch/stefan/7922901/working/3D/576' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=NN1) `REAL250005054437.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054437 none CC1=CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 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 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, 148, 81, 148, 43, 81, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 81, 81, 81, 43, 43, 28, 28, 7, 1, 165] 165 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: 517 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054437 none CC1=CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 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 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, 8, 8, 26, 26, 72, 99, 163, 163, 163, 165, 165, 165, 165, 165, 1, 1, 2, 2, 2, 1, 26, 26, 26, 72, 72, 99, 99, 163, 165, 1] 165 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: 639 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054437 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054437 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054437/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054437/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054437 Building REAL250005054438 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054438' /scratch/stefan/7922901/working/building/REAL250005054438 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054438 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054438/0 /scratch/stefan/7922901/working/building/REAL250005054438 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/577 `/scratch/stefan/7922901/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CS1) `REAL250005054438.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054438 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 21, 74, 108, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 21, 21, 21, 74, 74, 108, 108, 201, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 768 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: REAL250005054438 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 79, 144, 144, 201, 201, 201, 201, 79, 79, 79, 42, 42, 24, 24, 4, 1, 201, 200] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 610 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054438 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054438 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054438/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054438 Building REAL250005054439 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054439' /scratch/stefan/7922901/working/building/REAL250005054439 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054439 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054439/0 /scratch/stefan/7922901/working/building/REAL250005054439 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/578 `/scratch/stefan/7922901/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054439.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054439 none CCC=C(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 189, 123, 189, 68, 123, 36, 68, 22, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 189, 189, 189, 68, 68, 68, 36, 36, 22, 22, 5, 1] 201 rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 732 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054439 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054439 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054439/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054439 Building REAL250005054440 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054440' /scratch/stefan/7922901/working/building/REAL250005054440 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054440 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054440/0 /scratch/stefan/7922901/working/building/REAL250005054440 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/579 `/scratch/stefan/7922901/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)N=CO1) `REAL250005054440.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054440 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 132, 81, 132, 38, 81, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 81, 81, 81, 38, 38, 26, 26, 7, 1, 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]) total number of confs: 577 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054440 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 8, 8, 24, 24, 75, 111, 197, 197, 197, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 24, 24, 24, 75, 75, 111, 111, 197, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 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: 753 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054440 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054440 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054440/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054440 Building REAL250005054441 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054441' /scratch/stefan/7922901/working/building/REAL250005054441 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054441 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054441/0 /scratch/stefan/7922901/working/building/REAL250005054441 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/580 `/scratch/stefan/7922901/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(CC)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054441.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054441 none CCOC(CC)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [68, 67, 53, 43, 53, 66, 37, 43, 23, 37, 16, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 53, 66, 66, 66, 66, 66, 37, 37, 37, 23, 23, 16, 16, 6, 1] 71 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: 332 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054441 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054441 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054441/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054441 Building REAL250005054442 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054442' /scratch/stefan/7922901/working/building/REAL250005054442 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054442 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054442/0 /scratch/stefan/7922901/working/building/REAL250005054442 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/581 `/scratch/stefan/7922901/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(F)(F)F) `REAL250005054442.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054442 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(F)(F)F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [61, 35, 22, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 59, 98, 100, 119, 120, 119, 120, 61, 61, 61, 35, 35, 22, 22, 7, 1, 120, 120] 120 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 475 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054442 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054442 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054442/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054442 Building REAL250005054443 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054443' /scratch/stefan/7922901/working/building/REAL250005054443 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054443 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054443/0 /scratch/stefan/7922901/working/building/REAL250005054443 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/582 `/scratch/stefan/7922901/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054443.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054443 none COC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 97, 75, 97, 55, 75, 32, 55, 21, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 113, 113, 113, 97, 97, 97, 97, 55, 55, 55, 32, 32, 21, 21, 8, 1] 113 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: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054443 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054443 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054443/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054443 Building REAL250005054444 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054444' /scratch/stefan/7922901/working/building/REAL250005054444 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054444 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054444/0 /scratch/stefan/7922901/working/building/REAL250005054444 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/583 `/scratch/stefan/7922901/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054444.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054444 none CC(C)OCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 201, 105, 79, 67, 79, 43, 67, 26, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 105, 105, 67, 67, 67, 43, 43, 26, 26, 6, 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: 810 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054444 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054444 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054444/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054444 Building REAL250005054445 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054445' /scratch/stefan/7922901/working/building/REAL250005054445 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054445 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054445/0 /scratch/stefan/7922901/working/building/REAL250005054445 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/584 `/scratch/stefan/7922901/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054445.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054445 none CCCOCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 132, 76, 42, 37, 42, 27, 37, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 178, 178, 76, 76, 37, 37, 37, 27, 27, 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: 796 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054445 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054445 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054445/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054445 Building REAL250005054446 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054446' /scratch/stefan/7922901/working/building/REAL250005054446 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054446 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054446/0 /scratch/stefan/7922901/working/building/REAL250005054446 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/585 `/scratch/stefan/7922901/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCOC1) `REAL250005054446.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054446 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCOC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 22, 63, 94, 169, 169, 169, 174, 174, 174, 174, 174, 1, 6, 1, 1, 1, 1, 1, 22, 22, 22, 63, 63, 94, 94, 169, 174, 1, 1, 1, 1, 1, 1, 1] 174 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 660 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: REAL250005054446 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCOC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [83, 41, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 81, 150, 150, 174, 174, 174, 174, 83, 83, 83, 41, 41, 24, 24, 7, 1, 174, 174, 174, 174, 174, 174, 174] 174 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 610 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054446 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054446 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054446/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054446 Building REAL250005054447 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054447' /scratch/stefan/7922901/working/building/REAL250005054447 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054447 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054447/0 /scratch/stefan/7922901/working/building/REAL250005054447 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/586 `/scratch/stefan/7922901/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NN1C) `REAL250005054447.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054447 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NN1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 24, 69, 94, 201, 201, 201, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 69, 69, 94, 94, 201, 201, 1, 1, 2, 2, 2] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 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, 32, 33, 34]) total number of confs: 717 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: REAL250005054447 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NN1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 80, 169, 169, 201, 201, 201, 201, 201, 80, 80, 80, 39, 39, 25, 25, 5, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 603 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054447 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054447 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054447/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054447 Building REAL250005054448 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054448' /scratch/stefan/7922901/working/building/REAL250005054448 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054448 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054448/0 /scratch/stefan/7922901/working/building/REAL250005054448 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/587 `/scratch/stefan/7922901/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054448.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054448 none CCC(OC)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [90, 83, 63, 83, 91, 40, 63, 27, 40, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 83, 91, 91, 91, 40, 40, 40, 27, 27, 17, 17, 4, 1] 95 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: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054448 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054448 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054448/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054448 Building REAL250005054449 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054449' /scratch/stefan/7922901/working/building/REAL250005054449 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054449 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054449/0 /scratch/stefan/7922901/working/building/REAL250005054449 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/588 `/scratch/stefan/7922901/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054449.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054449 none COCCCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 102, 88, 33, 29, 33, 25, 29, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 117, 117, 109, 109, 89, 89, 29, 29, 29, 25, 25, 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: 1001 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054449 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054449 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054449/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054449 Building REAL250005054450 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054450' /scratch/stefan/7922901/working/building/REAL250005054450 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054450 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054450/0 /scratch/stefan/7922901/working/building/REAL250005054450 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/589 `/scratch/stefan/7922901/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054450.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054450 none CCCC(C)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 171, 123, 171, 47, 43, 47, 32, 43, 20, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 171, 171, 171, 171, 124, 124, 43, 43, 43, 32, 32, 20, 20, 5, 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: 920 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054450 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054450 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054450/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054450 Building REAL250005054451 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054451' /scratch/stefan/7922901/working/building/REAL250005054451 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054451 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054451/0 /scratch/stefan/7922901/working/building/REAL250005054451 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/590 `/scratch/stefan/7922901/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054451.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054451 none COC(C)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 116, 91, 116, 62, 53, 62, 30, 53, 19, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 117, 117, 117, 116, 116, 116, 116, 91, 91, 53, 53, 53, 30, 30, 19, 19, 4, 1] 117 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: 522 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054451 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054451 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054451/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054451 Building REAL250005054452 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054452' /scratch/stefan/7922901/working/building/REAL250005054452 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054452 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054452/0 /scratch/stefan/7922901/working/building/REAL250005054452 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/591 `/scratch/stefan/7922901/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054452.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054452 none C=CCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 154, 83, 69, 83, 36, 69, 22, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 154, 154, 69, 69, 69, 36, 36, 22, 22, 6, 1] 186 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 777 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054452 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054452 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054452/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054452 Building REAL250005054453 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054453' /scratch/stefan/7922901/working/building/REAL250005054453 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054453 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054453/0 /scratch/stefan/7922901/working/building/REAL250005054453 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/592 `/scratch/stefan/7922901/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COCCC1) `REAL250005054453.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054453 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 53, 88, 176, 178, 177, 184, 184, 184, 184, 184, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 53, 53, 88, 88, 178, 184, 1, 1, 1, 1, 1, 1, 1] 184 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 692 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: REAL250005054453 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [71, 42, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 71, 124, 124, 184, 184, 184, 184, 184, 71, 71, 71, 42, 42, 27, 27, 8, 1, 184, 184, 184, 184, 184, 184, 184] 184 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 545 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054453 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054453 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054453/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054453 Building REAL250005054454 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054454' /scratch/stefan/7922901/working/building/REAL250005054454 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054454 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054454/0 /scratch/stefan/7922901/working/building/REAL250005054454 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/593 `/scratch/stefan/7922901/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCOC1) `REAL250005054454.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054454 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCOC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 53, 99, 199, 199, 199, 201, 201, 201, 201, 201, 1, 5, 1, 1, 1, 1, 1, 1, 17, 17, 17, 53, 53, 99, 99, 199, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 772 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054454 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCOC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 75, 161, 161, 201, 201, 201, 201, 201, 75, 75, 75, 40, 40, 22, 22, 6, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 689 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054454 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054454 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054454/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054454 Building REAL250005054455 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054455' /scratch/stefan/7922901/working/building/REAL250005054455 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054455 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054455/0 /scratch/stefan/7922901/working/building/REAL250005054455 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/594 `/scratch/stefan/7922901/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054455.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054455 none CCOCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 112, 85, 43, 39, 43, 27, 39, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 112, 112, 85, 85, 39, 39, 39, 27, 27, 18, 18, 4, 1] 125 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: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054455 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054455 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054455/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054455 Building REAL250005054456 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054456' /scratch/stefan/7922901/working/building/REAL250005054456 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054456 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054456/0 /scratch/stefan/7922901/working/building/REAL250005054456 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/595 `/scratch/stefan/7922901/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CSC=N1) `REAL250005054456.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054456 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CSC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 10, 23, 61, 95, 187, 187, 187, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 23, 23, 23, 61, 61, 95, 95, 187, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 691 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054456 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CSC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 52, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 107, 192, 192, 201, 201, 201, 201, 107, 107, 107, 52, 52, 34, 34, 11, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 675 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054456 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054456 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054456/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054456 Building REAL250005054457 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054457' /scratch/stefan/7922901/working/building/REAL250005054457 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054457 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054457/0 /scratch/stefan/7922901/working/building/REAL250005054457 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/596 `/scratch/stefan/7922901/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054457.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054457 none COCC(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 99, 73, 99, 59, 73, 32, 59, 19, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 99, 99, 99, 99, 59, 59, 59, 32, 32, 19, 19, 4, 1] 132 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: 574 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054457 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054457 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054457/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054457 Building REAL250005054458 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054458' /scratch/stefan/7922901/working/building/REAL250005054458 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054458 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054458/0 /scratch/stefan/7922901/working/building/REAL250005054458 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/597 `/scratch/stefan/7922901/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054458.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054458 none C=CCOCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 116, 68, 41, 36, 41, 25, 36, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 68, 68, 36, 36, 36, 25, 25, 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: 786 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054458 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054458 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054458/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054458 Building REAL250005054459 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054459' /scratch/stefan/7922901/working/building/REAL250005054459 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054459 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054459/0 /scratch/stefan/7922901/working/building/REAL250005054459 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/598 `/scratch/stefan/7922901/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COC=N1) `REAL250005054459.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054459 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [25, 10, 25, 65, 95, 189, 189, 189, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 25, 25, 25, 65, 65, 95, 95, 189, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005054459 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [101, 54, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 99, 189, 189, 201, 201, 201, 201, 101, 101, 101, 54, 54, 32, 32, 9, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054459 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054459 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054459/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054459 Building REAL250005054460 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054460' /scratch/stefan/7922901/working/building/REAL250005054460 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054460 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054460/0 /scratch/stefan/7922901/working/building/REAL250005054460 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/599 `/scratch/stefan/7922901/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCC(=O)N1) `REAL250005054460.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054460 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 4, 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: [22, 6, 22, 63, 97, 162, 162, 162, 165, 165, 165, 165, 165, 1, 6, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 63, 63, 97, 97, 162, 165, 1, 1, 1, 1, 1] 165 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 655 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: REAL250005054460 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 4, 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: [76, 36, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 75, 138, 138, 165, 165, 165, 165, 165, 165, 76, 76, 76, 36, 36, 21, 21, 7, 1, 165, 165, 165, 165, 165] 165 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 567 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054460 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054460 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054460/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054460 Building REAL250005054461 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054461' /scratch/stefan/7922901/working/building/REAL250005054461 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054461 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054461/0 /scratch/stefan/7922901/working/building/REAL250005054461 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/600 `/scratch/stefan/7922901/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=CN1) `REAL250005054461.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054461 none CC1=NC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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 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, 108, 65, 108, 41, 65, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 65, 65, 65, 41, 41, 27, 27, 7, 1, 130, 130] 130 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: 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: REAL250005054461 none CC1=NC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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 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, 8, 8, 21, 21, 54, 70, 128, 128, 128, 130, 130, 130, 130, 130, 1, 1, 2, 2, 2, 21, 21, 21, 54, 54, 70, 70, 128, 130, 1, 1] 130 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: 471 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054461 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054461/1 /scratch/stefan/7922901/working/building/REAL250005054461 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/601 `/scratch/stefan/7922901/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005054461.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054461 none CC1=NC=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 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 201 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, 166, 99, 166, 55, 99, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 99, 99, 99, 55, 55, 30, 30, 8, 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: 651 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: REAL250005054461 none CC1=NC=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 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 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, 31, 31, 73, 107, 187, 187, 187, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 31, 31, 31, 73, 73, 107, 107, 187, 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: 739 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054461 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054461 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054461/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054461/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054461 Building REAL250005054462 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054462' /scratch/stefan/7922901/working/building/REAL250005054462 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054462 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054462/0 /scratch/stefan/7922901/working/building/REAL250005054462 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/602 `/scratch/stefan/7922901/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC[N@@H+]1C) `REAL250005054462.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054462 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC[N@@H+]1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 7, 7, 9, 9, 9, 12, 12, 12, 12, 12, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 9, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 12 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40]) total number of confs: 46 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054462 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC[N@@H+]1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 8, 8, 4, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 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: 46 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054462 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054462/1 /scratch/stefan/7922901/working/building/REAL250005054462 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/603 `/scratch/stefan/7922901/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC[N@H+]1C) `REAL250005054462.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054462 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC[N@H+]1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 3 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054462 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC[N@H+]1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 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: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054462 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054462 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054462/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054462/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054462 Building REAL250005054463 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054463' /scratch/stefan/7922901/working/building/REAL250005054463 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054463 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054463/0 /scratch/stefan/7922901/working/building/REAL250005054463 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/604 `/scratch/stefan/7922901/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054463.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054463 none CCC(=O)NCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 49, 49, 49, 33, 21, 17, 21, 17, 17, 11, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 49, 33, 33, 17, 17, 17, 17, 17, 11, 11, 4, 1] 69 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: 311 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054463 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054463 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054463/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054463 Building REAL250005054464 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054464' /scratch/stefan/7922901/working/building/REAL250005054464 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054464 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054464/0 /scratch/stefan/7922901/working/building/REAL250005054464 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/605 `/scratch/stefan/7922901/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CC(C)(C)C) `REAL250005054464.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054464 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CC(C)(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 112, 112, 189, 189, 201, 201, 201, 65, 65, 65, 27, 27, 16, 16, 4, 1, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 710 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054464 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054464 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054464/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054464 Building REAL250005054465 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054465' /scratch/stefan/7922901/working/building/REAL250005054465 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054465 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054465/0 /scratch/stefan/7922901/working/building/REAL250005054465 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/606 `/scratch/stefan/7922901/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054465.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054465 none CC(C#N)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 59, 74, 74, 47, 59, 29, 47, 20, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 47, 47, 47, 29, 29, 20, 20, 5, 1] 74 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: 316 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054465 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054465 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054465/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054465 Building REAL250005054466 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054466' /scratch/stefan/7922901/working/building/REAL250005054466 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054466 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054466/0 /scratch/stefan/7922901/working/building/REAL250005054466 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/607 `/scratch/stefan/7922901/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054466.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054466 none CCCC(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 174, 145, 100, 145, 77, 100, 44, 77, 23, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 178, 176, 176, 145, 145, 145, 145, 77, 77, 77, 44, 44, 23, 23, 6, 1] 180 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: 843 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054466 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054466 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054466/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054466 Building REAL250005054467 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054467' /scratch/stefan/7922901/working/building/REAL250005054467 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054467 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054467/0 /scratch/stefan/7922901/working/building/REAL250005054467 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/608 `/scratch/stefan/7922901/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(=O)C(C)(C)C) `REAL250005054467.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054467 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 21, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 73, 143, 143, 173, 173, 201, 201, 201, 73, 73, 73, 37, 37, 21, 21, 6, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 758 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054467 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054467 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054467/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054467 Building REAL250005054468 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054468' /scratch/stefan/7922901/working/building/REAL250005054468 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054468 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054468/0 /scratch/stefan/7922901/working/building/REAL250005054468 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/609 `/scratch/stefan/7922901/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC1CC1) `REAL250005054468.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054468 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 31, 73, 115, 201, 201, 201, 201, 201, 201, 201, 201, 5, 19, 3, 1, 1, 1, 1, 31, 31, 31, 73, 73, 115, 115, 201, 201, 5, 5, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 788 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: REAL250005054468 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 55, 91, 91, 112, 122, 201, 201, 55, 55, 55, 26, 26, 14, 14, 4, 1, 112, 112, 122, 122, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 788 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054468 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054468 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054468/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054468 Building REAL250005054469 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054469' /scratch/stefan/7922901/working/building/REAL250005054469 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054469 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054469/0 /scratch/stefan/7922901/working/building/REAL250005054469 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/610 `/scratch/stefan/7922901/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054469.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054469 none CCCCOCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 102, 72, 19, 19, 19, 17, 19, 10, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 125, 125, 72, 72, 19, 19, 19, 17, 17, 10, 10, 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/7922901/working/building/REAL250005054469 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054469 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054469/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054469 Building REAL250005054470 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054470' /scratch/stefan/7922901/working/building/REAL250005054470 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054470 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054470/0 /scratch/stefan/7922901/working/building/REAL250005054470 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/611 `/scratch/stefan/7922901/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NOC=C1) `REAL250005054470.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054470 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NOC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 20, 38, 82, 118, 201, 201, 201, 201, 201, 201, 201, 201, 5, 20, 1, 1, 1, 1, 1, 1, 38, 38, 38, 82, 82, 118, 118, 201, 201, 5, 5, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 782 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054470 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NOC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 26, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 125, 125, 188, 201, 201, 201, 201, 65, 65, 65, 26, 26, 14, 14, 4, 1, 188, 188, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 745 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054470 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054470 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054470/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054470 Building REAL250005054471 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054471' /scratch/stefan/7922901/working/building/REAL250005054471 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054471 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054471/0 /scratch/stefan/7922901/working/building/REAL250005054471 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/612 `/scratch/stefan/7922901/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CCOC1) `REAL250005054471.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054471 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CCOC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [30, 13, 30, 66, 90, 190, 190, 190, 190, 190, 190, 190, 190, 5, 13, 1, 1, 1, 1, 1, 1, 30, 30, 30, 66, 66, 90, 90, 190, 190, 5, 5, 1, 1, 1, 1, 1, 1, 1] 190 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL250005054471 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CCOC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [56, 26, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 56, 118, 118, 126, 190, 190, 190, 190, 56, 56, 56, 26, 26, 17, 17, 4, 1, 126, 126, 190, 190, 190, 190, 190, 190, 190] 190 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054471 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054471 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054471/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054471 Building REAL250005054472 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054472' /scratch/stefan/7922901/working/building/REAL250005054472 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054472 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054472/0 /scratch/stefan/7922901/working/building/REAL250005054472 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/613 `/scratch/stefan/7922901/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC=CC1) `REAL250005054472.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054472 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC=CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 6, 23, 61, 100, 191, 191, 191, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 23, 23, 23, 61, 61, 100, 100, 191, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 745 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054472 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC=CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 45, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 92, 161, 162, 201, 201, 201, 201, 94, 94, 94, 45, 45, 25, 25, 7, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 707 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054472 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054472 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054472/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054472 Building REAL250005054473 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054473' /scratch/stefan/7922901/working/building/REAL250005054473 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054473 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054473/0 /scratch/stefan/7922901/working/building/REAL250005054473 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/614 `/scratch/stefan/7922901/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NNC=C1) `REAL250005054473.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054473 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NNC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 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: [37, 23, 37, 81, 113, 201, 201, 201, 201, 201, 201, 201, 201, 8, 23, 1, 1, 1, 1, 1, 1, 37, 37, 37, 81, 81, 113, 113, 201, 201, 8, 8, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 783 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054473 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NNC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 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: [61, 32, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 61, 110, 110, 186, 201, 201, 201, 201, 61, 61, 61, 32, 32, 20, 20, 4, 1, 186, 186, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 769 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054473 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054473/1 /scratch/stefan/7922901/working/building/REAL250005054473 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/615 `/scratch/stefan/7922901/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CC=NN1) `REAL250005054473.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054473 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CC=NN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 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: [54, 28, 54, 103, 124, 201, 200, 201, 201, 201, 201, 201, 201, 8, 28, 1, 1, 1, 1, 1, 1, 54, 54, 54, 103, 103, 125, 125, 201, 201, 8, 8, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 767 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: REAL250005054473 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CC=NN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 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: [61, 27, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 61, 127, 127, 173, 201, 201, 201, 201, 61, 61, 61, 27, 27, 18, 18, 4, 1, 173, 173, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 714 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054473 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054473 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054473/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054473/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054473 Building REAL250005054474 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054474' /scratch/stefan/7922901/working/building/REAL250005054474 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054474 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054474/0 /scratch/stefan/7922901/working/building/REAL250005054474 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/616 `/scratch/stefan/7922901/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CCC1) `REAL250005054474.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054474 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 31, 69, 96, 201, 201, 201, 201, 201, 201, 201, 201, 5, 16, 1, 1, 1, 1, 1, 31, 31, 31, 69, 69, 96, 96, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 710 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054474 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 58, 114, 114, 121, 201, 201, 201, 58, 58, 58, 30, 30, 19, 19, 4, 1, 121, 121, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 745 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054474 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054474 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054474/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054474 Building REAL250005054475 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054475' /scratch/stefan/7922901/working/building/REAL250005054475 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054475 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054475/0 /scratch/stefan/7922901/working/building/REAL250005054475 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/617 `/scratch/stefan/7922901/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)OC=N1) `REAL250005054475.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054475 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 126, 76, 126, 36, 76, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 76, 76, 76, 36, 36, 22, 22, 5, 1, 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]) total number of confs: 569 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054475 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 8, 8, 23, 23, 72, 102, 197, 197, 197, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 23, 23, 23, 72, 72, 102, 102, 197, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 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: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054475 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054475 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054475/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054475 Building REAL250005054476 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054476' /scratch/stefan/7922901/working/building/REAL250005054476 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054476 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054476/0 /scratch/stefan/7922901/working/building/REAL250005054476 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/618 `/scratch/stefan/7922901/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005054476.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054476 none CC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 8, 8, 16, 16, 34, 48, 82, 82, 82, 86, 86, 86, 86, 86, 1, 1, 1, 3, 3, 3, 3, 16, 16, 16, 34, 34, 48, 48, 82, 86, 1, 1, 1, 1, 1] 86 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: 309 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054476 none CC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 70, 55, 70, 31, 55, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 86, 55, 55, 55, 31, 31, 21, 21, 8, 1, 86, 86, 86, 86, 86] 86 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: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054476 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054476 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054476/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054476 Building REAL250005054477 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054477' /scratch/stefan/7922901/working/building/REAL250005054477 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054477 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054477/0 /scratch/stefan/7922901/working/building/REAL250005054477 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/619 `/scratch/stefan/7922901/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1C2CCCC21) `REAL250005054477.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054477 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1C2CCCC21 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 5, 9, 31, 47, 93, 93, 93, 99, 99, 99, 99, 99, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 31, 31, 47, 47, 93, 99, 1, 1, 1, 1, 1, 1, 1, 1, 1] 99 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 353 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: REAL250005054477 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1C2CCCC21 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [59, 31, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 59, 87, 87, 99, 99, 99, 99, 99, 59, 59, 59, 31, 31, 20, 20, 7, 1, 99, 99, 99, 99, 99, 99, 99, 99, 99] 99 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 362 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054477 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054477 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054477/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054477 Building REAL250005054478 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054478' /scratch/stefan/7922901/working/building/REAL250005054478 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054478 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054478/0 /scratch/stefan/7922901/working/building/REAL250005054478 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/620 `/scratch/stefan/7922901/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC1CCC1) `REAL250005054478.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054478 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 40, 91, 127, 201, 201, 201, 201, 201, 201, 201, 201, 11, 24, 6, 1, 1, 1, 1, 1, 40, 40, 40, 91, 91, 127, 127, 201, 201, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 804 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: REAL250005054478 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 57, 85, 85, 90, 125, 201, 201, 201, 57, 57, 57, 34, 34, 22, 22, 4, 1, 90, 90, 125, 125, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 825 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054478 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054478 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054478/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054478 Building REAL250005054479 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054479' /scratch/stefan/7922901/working/building/REAL250005054479 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054479 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054479/0 /scratch/stefan/7922901/working/building/REAL250005054479 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/621 `/scratch/stefan/7922901/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C=CN1) `REAL250005054479.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054479 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 137, 75, 137, 42, 75, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 182, 182, 75, 75, 75, 42, 42, 27, 27, 7, 1, 182, 182, 182] 182 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: 546 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: REAL250005054479 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 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 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 25, 25, 69, 93, 176, 178, 176, 182, 182, 182, 182, 182, 1, 1, 1, 2, 2, 2, 25, 25, 25, 69, 69, 93, 93, 178, 182, 1, 1, 1] 182 rigid atoms, others: [0, 1, 2, 3, 35, 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: 671 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054479 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054479 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054479/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054479 Building REAL250005054480 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054480' /scratch/stefan/7922901/working/building/REAL250005054480 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054480 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054480/0 /scratch/stefan/7922901/working/building/REAL250005054480 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/622 `/scratch/stefan/7922901/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054480.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054480 none CC=C(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 91, 137, 63, 91, 36, 63, 24, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 137, 137, 63, 63, 63, 36, 36, 24, 24, 7, 1] 137 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: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054480 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054480 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054480/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054480 Building REAL250005054481 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054481' /scratch/stefan/7922901/working/building/REAL250005054481 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054481 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054481/0 /scratch/stefan/7922901/working/building/REAL250005054481 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/623 `/scratch/stefan/7922901/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054481.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054481 none CC1CC(C(=O)N(C)CCNC(=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', '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, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 116, 71, 116, 39, 71, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 142, 142, 142, 142, 71, 71, 71, 39, 39, 28, 28, 10, 1, 142, 142] 142 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: 500 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: REAL250005054481 none CC1CC(C(=O)N(C)CCNC(=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', '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, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 17, 17, 47, 70, 136, 136, 136, 142, 142, 142, 142, 142, 1, 2, 2, 2, 1, 1, 1, 1, 17, 17, 17, 47, 47, 70, 70, 136, 142, 1, 1] 142 rigid atoms, others: [0, 1, 2, 3, 4, 37, 19, 23, 24, 25, 26, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 523 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054481 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054481 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054481/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054481 Building REAL250005054482 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054482' /scratch/stefan/7922901/working/building/REAL250005054482 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054482 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054482/0 /scratch/stefan/7922901/working/building/REAL250005054482 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/624 `/scratch/stefan/7922901/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=C1CCC1) `REAL250005054482.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054482 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=C1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 9, 40, 94, 121, 201, 201, 201, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 40, 40, 40, 94, 94, 121, 121, 201, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 756 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: REAL250005054482 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=C1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 33, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 70, 145, 145, 201, 201, 201, 201, 70, 70, 70, 33, 33, 17, 17, 5, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 684 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054482 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054482 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054482/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054482 Building REAL250005054483 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054483' /scratch/stefan/7922901/working/building/REAL250005054483 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054483 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054483/0 /scratch/stefan/7922901/working/building/REAL250005054483 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/625 `/scratch/stefan/7922901/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)CC) `REAL250005054483.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054483 none CCC(=CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 140, 140, 77, 56, 77, 32, 56, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 140, 175, 165, 165, 165, 165, 165, 140, 56, 56, 56, 32, 32, 18, 18, 4, 1, 175, 175, 175, 175, 175] 201 rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 858 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054483 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054483 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054483/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054483 Building REAL250005054484 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054484' /scratch/stefan/7922901/working/building/REAL250005054484 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054484 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054484/0 /scratch/stefan/7922901/working/building/REAL250005054484 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/626 `/scratch/stefan/7922901/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054484.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054484 none CC(C)=C(F)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 1, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 89, 125, 60, 89, 37, 60, 26, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 125, 60, 60, 60, 37, 37, 26, 26, 9, 1] 125 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: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054484 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054484 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054484/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054484 Building REAL250005054485 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054485' /scratch/stefan/7922901/working/building/REAL250005054485 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054485 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054485/0 /scratch/stefan/7922901/working/building/REAL250005054485 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/627 `/scratch/stefan/7922901/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCCC1) `REAL250005054485.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054485 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 20, 53, 76, 136, 136, 136, 140, 140, 140, 140, 140, 1, 9, 1, 1, 1, 1, 1, 20, 20, 20, 53, 53, 76, 76, 136, 140, 1, 1, 1, 1, 1, 1, 1] 140 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 520 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: REAL250005054485 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [80, 43, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 79, 140, 140, 140, 140, 140, 140, 80, 80, 80, 43, 43, 26, 26, 7, 1, 140, 140, 140, 140, 140, 140, 140] 140 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 488 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054485 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054485 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054485/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054485 Building REAL250005054486 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054486' /scratch/stefan/7922901/working/building/REAL250005054486 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054486 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054486/0 /scratch/stefan/7922901/working/building/REAL250005054486 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/628 `/scratch/stefan/7922901/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN(C)C=C1) `REAL250005054486.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054486 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN(C)C=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 11, 30, 74, 103, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 30, 30, 30, 74, 74, 103, 103, 201, 201, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [34, 35, 13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 745 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: REAL250005054486 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN(C)C=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 30, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 63, 125, 125, 201, 201, 201, 201, 201, 63, 63, 63, 30, 30, 18, 18, 4, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 566 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054486 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054486 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054486/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054486 Building REAL250005054487 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054487' /scratch/stefan/7922901/working/building/REAL250005054487 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054487 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054487/0 /scratch/stefan/7922901/working/building/REAL250005054487 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/629 `/scratch/stefan/7922901/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN(C)C=N1) `REAL250005054487.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054487 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN(C)C=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 31, 78, 106, 193, 193, 193, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 31, 78, 78, 106, 106, 193, 201, 1, 2, 2, 2, 1] 201 rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 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: REAL250005054487 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN(C)C=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 49, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 96, 179, 179, 201, 201, 201, 201, 201, 96, 96, 96, 49, 49, 32, 32, 9, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 629 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054487 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054487 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054487/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054487 Building REAL250005054488 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054488' /scratch/stefan/7922901/working/building/REAL250005054488 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054488 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054488/0 /scratch/stefan/7922901/working/building/REAL250005054488 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/630 `/scratch/stefan/7922901/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCCO1) `REAL250005054488.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054488 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 41, 61, 114, 114, 114, 124, 124, 124, 124, 124, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 41, 41, 61, 61, 114, 124, 1, 1, 1, 1, 1, 1, 1, 1, 1] 124 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 429 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: REAL250005054488 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [76, 41, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 76, 117, 117, 124, 124, 124, 124, 124, 76, 76, 76, 41, 41, 27, 27, 10, 1, 124, 124, 124, 124, 124, 124, 124, 124, 124] 124 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 427 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054488 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054488 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054488/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054488 Building REAL250005054489 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054489' /scratch/stefan/7922901/working/building/REAL250005054489 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054489 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054489/0 /scratch/stefan/7922901/working/building/REAL250005054489 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/631 `/scratch/stefan/7922901/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC1(C)C) `REAL250005054489.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054489 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC1(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 37, 55, 88, 88, 88, 91, 91, 91, 91, 91, 1, 5, 1, 1, 1, 1, 1, 13, 13, 13, 37, 37, 55, 55, 88, 91, 1, 1, 1, 2, 2, 2, 2, 2, 2] 91 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 360 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: REAL250005054489 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC1(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 32, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 51, 85, 85, 91, 91, 91, 91, 52, 52, 52, 32, 32, 22, 22, 7, 1, 91, 91, 91, 91, 91, 91, 91, 91, 91] 91 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 320 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054489 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054489 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054489/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054489 Building REAL250005054490 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054490' /scratch/stefan/7922901/working/building/REAL250005054490 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054490 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054490/0 /scratch/stefan/7922901/working/building/REAL250005054490 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/632 `/scratch/stefan/7922901/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054490.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054490 none CCC(C)OCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 159, 186, 90, 55, 51, 55, 32, 51, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 186, 186, 186, 186, 90, 90, 51, 51, 51, 32, 32, 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: 724 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054490 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054490 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054490/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054490 Building REAL250005054491 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054491' /scratch/stefan/7922901/working/building/REAL250005054491 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054491 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054491/0 /scratch/stefan/7922901/working/building/REAL250005054491 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/633 `/scratch/stefan/7922901/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CC1(C)C) `REAL250005054491.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054491 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CC1(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 37, 55, 88, 88, 88, 91, 91, 91, 91, 91, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 37, 37, 55, 55, 88, 91, 1, 1, 2, 2, 2, 2, 2, 2] 91 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 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, 32, 33, 34, 35, 36, 37]) total number of confs: 360 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: REAL250005054491 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CC1(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 32, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 52, 85, 85, 91, 91, 91, 91, 91, 52, 52, 52, 32, 32, 22, 22, 7, 1, 91, 91, 91, 91, 91, 91, 91, 91] 91 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 318 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054491 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054491 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054491/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054491 Building REAL250005054492 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054492' /scratch/stefan/7922901/working/building/REAL250005054492 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054492 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054492/0 /scratch/stefan/7922901/working/building/REAL250005054492 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/634 `/scratch/stefan/7922901/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCCO1) `REAL250005054492.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054492 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 21, 50, 73, 140, 140, 140, 153, 153, 153, 153, 153, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 50, 50, 73, 73, 140, 153, 1, 1, 1, 1, 1, 1] 153 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 525 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: REAL250005054492 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [92, 51, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 92, 145, 145, 153, 153, 153, 153, 153, 92, 92, 92, 51, 51, 37, 37, 11, 1, 153, 153, 153, 153, 153, 153] 153 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 517 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054492 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054492 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054492/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054492 Building REAL250005054493 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054493' /scratch/stefan/7922901/working/building/REAL250005054493 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054493 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054493/0 /scratch/stefan/7922901/working/building/REAL250005054493 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/635 `/scratch/stefan/7922901/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054493.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054493 none C#CCCCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 127, 116, 102, 50, 39, 50, 26, 39, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 199, 201, 201, 129, 129, 117, 117, 103, 103, 39, 39, 39, 26, 26, 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: 931 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054493 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054493 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054493/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054493 Building REAL250005054494 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054494' /scratch/stefan/7922901/working/building/REAL250005054494 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054494 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054494/0 /scratch/stefan/7922901/working/building/REAL250005054494 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/636 `/scratch/stefan/7922901/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)COC(C)(C)C) `REAL250005054494.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054494 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)COC(C)(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [77, 43, 29, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 77, 113, 113, 131, 132, 137, 137, 137, 77, 77, 77, 43, 43, 29, 29, 7, 1, 131, 131, 137, 137, 137, 137, 137, 137, 137, 137, 137] 137 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 537 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054494 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054494 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054494/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054494 Building REAL250005054495 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054495' /scratch/stefan/7922901/working/building/REAL250005054495 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054495 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054495/0 /scratch/stefan/7922901/working/building/REAL250005054495 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/637 `/scratch/stefan/7922901/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054495.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054495 none CCNC(=O)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 104, 104, 81, 104, 45, 45, 45, 29, 45, 22, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 104, 81, 81, 45, 45, 45, 29, 29, 22, 22, 9, 1] 143 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: 646 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054495 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054495 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054495/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054495 Building REAL250005054496 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054496' /scratch/stefan/7922901/working/building/REAL250005054496 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054496 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054496/0 /scratch/stefan/7922901/working/building/REAL250005054496 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/638 `/scratch/stefan/7922901/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054496.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054496 none COC(C)CCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 58, 82, 44, 16, 15, 16, 14, 15, 9, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82, 66, 66, 45, 45, 15, 15, 15, 14, 14, 9, 9, 4, 1] 82 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: 442 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054496 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054496 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054496/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054496 Building REAL250005054497 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054497' /scratch/stefan/7922901/working/building/REAL250005054497 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054497 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054497/0 /scratch/stefan/7922901/working/building/REAL250005054497 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/639 `/scratch/stefan/7922901/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CN=C1) `REAL250005054497.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054497 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CN=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 3, 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: [15, 6, 15, 45, 68, 136, 136, 136, 138, 138, 138, 138, 138, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 45, 45, 68, 68, 136, 138, 1, 1, 1] 138 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 506 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: REAL250005054497 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CN=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [81, 41, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 81, 138, 138, 138, 138, 138, 138, 138, 81, 81, 81, 41, 41, 26, 26, 6, 1, 138, 138, 138] 138 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 460 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054497 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054497 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054497/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054497 Building REAL250005054498 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054498' /scratch/stefan/7922901/working/building/REAL250005054498 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054498 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054498/0 /scratch/stefan/7922901/working/building/REAL250005054498 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/640 `/scratch/stefan/7922901/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCOCC1) `REAL250005054498.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054498 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCOCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 11, 39, 63, 123, 123, 123, 132, 132, 132, 132, 132, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 39, 39, 63, 63, 123, 132, 1, 1, 1, 1, 1, 1, 1] 132 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 491 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054498 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCOCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [78, 47, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 78, 132, 132, 132, 132, 132, 132, 132, 78, 78, 78, 47, 47, 32, 32, 9, 1, 132, 132, 132, 132, 132, 132, 132] 132 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 455 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054498 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054498 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054498/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054498 Building REAL250005054499 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054499' /scratch/stefan/7922901/working/building/REAL250005054499 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054499 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054499/0 /scratch/stefan/7922901/working/building/REAL250005054499 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/641 `/scratch/stefan/7922901/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=COC=C1) `REAL250005054499.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054499 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=COC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 21, 53, 106, 130, 201, 201, 201, 201, 201, 201, 201, 201, 4, 21, 1, 1, 1, 1, 1, 1, 54, 54, 54, 106, 106, 130, 130, 201, 201, 4, 4, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 778 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054499 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=COC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 23, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 42, 74, 74, 115, 201, 201, 201, 201, 42, 42, 42, 23, 23, 14, 14, 4, 1, 115, 115, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 606 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054499 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054499 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054499/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054499 Building REAL250005054500 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054500' /scratch/stefan/7922901/working/building/REAL250005054500 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054500 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054500/0 /scratch/stefan/7922901/working/building/REAL250005054500 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/642 `/scratch/stefan/7922901/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=CO1) `REAL250005054500.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054500 none CC1=NC(C(=O)N(C)CCNC(=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', '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, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 116, 71, 116, 40, 71, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 138, 71, 71, 71, 40, 40, 27, 27, 7, 1, 138] 138 rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33]) 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: REAL250005054500 none CC1=NC(C(=O)N(C)CCNC(=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', '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, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 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: [1, 1, 1, 1, 1, 8, 8, 23, 23, 58, 79, 134, 134, 134, 138, 138, 138, 138, 138, 1, 1, 2, 2, 2, 23, 23, 23, 58, 58, 79, 79, 134, 138, 1] 138 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: 512 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054500 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054500 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054500/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054500 Building REAL250005054501 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054501' /scratch/stefan/7922901/working/building/REAL250005054501 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054501 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054501/0 /scratch/stefan/7922901/working/building/REAL250005054501 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/643 `/scratch/stefan/7922901/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054501.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054501 none C[C@H](NC(N)=O)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 71, 95, 95, 95, 95, 95, 65, 71, 34, 65, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 65, 65, 65, 34, 34, 20, 20, 4, 1] 95 rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 386 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054501 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054501 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054501/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054501 Building REAL250005054502 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054502' /scratch/stefan/7922901/working/building/REAL250005054502 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054502 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054502/0 /scratch/stefan/7922901/working/building/REAL250005054502 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/644 `/scratch/stefan/7922901/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=CO1) `REAL250005054502.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054502 none CC1=CC(C(=O)N(C)CCNC(=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', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 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, 137, 79, 137, 42, 79, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 79, 79, 79, 42, 42, 24, 24, 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: 599 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054502 none CC1=CC(C(=O)N(C)CCNC(=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', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 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, 11, 11, 29, 29, 71, 95, 199, 199, 199, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 29, 29, 29, 71, 71, 95, 95, 199, 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: 723 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054502 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054502 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054502/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054502 Building REAL250005054503 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054503' /scratch/stefan/7922901/working/building/REAL250005054503 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054503 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054503/0 /scratch/stefan/7922901/working/building/REAL250005054503 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/645 `/scratch/stefan/7922901/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054503.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054503 none CCC(C)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 139, 184, 59, 57, 59, 40, 57, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 183, 184, 184, 184, 140, 140, 57, 57, 57, 40, 40, 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: 929 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054503 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054503 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054503/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054503 Building REAL250005054504 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054504' /scratch/stefan/7922901/working/building/REAL250005054504 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054504 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054504/0 /scratch/stefan/7922901/working/building/REAL250005054504 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/646 `/scratch/stefan/7922901/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054504.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054504 none C#CCCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 97, 89, 44, 39, 44, 29, 39, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 191, 190, 113, 113, 90, 90, 39, 39, 39, 29, 29, 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: 960 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054504 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054504 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054504/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054504 Building REAL250005054505 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054505' /scratch/stefan/7922901/working/building/REAL250005054505 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054505 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054505/0 /scratch/stefan/7922901/working/building/REAL250005054505 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/647 `/scratch/stefan/7922901/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054505.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054505 none C=CC(C)(O)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 17, 23, 23, 11, 11, 11, 10, 11, 8, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 69, 17, 17, 11, 11, 11, 10, 10, 8, 8, 2, 1] 69 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: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054505 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054505 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054505/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054505 Building REAL250005054506 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054506' /scratch/stefan/7922901/working/building/REAL250005054506 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054506 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054506/0 /scratch/stefan/7922901/working/building/REAL250005054506 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/648 `/scratch/stefan/7922901/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(C)(C)O) `REAL250005054506.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054506 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(C)(C)O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 405 conformations in input total number of sets (complete confs): 405 using faster count positions algorithm for large data unique positions, atoms: [69, 41, 24, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 68, 121, 122, 135, 135, 135, 135, 69, 69, 69, 41, 41, 24, 24, 7, 1, 135, 135, 135, 135, 135, 135, 135, 135, 405] 405 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 908 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054506 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054506 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054506/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054506 Building REAL250005054507 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054507' /scratch/stefan/7922901/working/building/REAL250005054507 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054507 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054507/0 /scratch/stefan/7922901/working/building/REAL250005054507 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/649 `/scratch/stefan/7922901/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005054507.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054507 none COC(C(=O)N(C)CCNC(=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', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 7, 1, 7, 21, 21, 40, 40, 74, 92, 124, 125, 124, 126, 126, 126, 126, 126, 1, 1, 1, 15, 15, 15, 7, 40, 40, 40, 74, 74, 92, 92, 125, 126, 1, 1, 1, 1, 1] 127 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: 527 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: REAL250005054507 none COC(C(=O)N(C)CCNC(=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', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [122, 112, 71, 45, 71, 31, 45, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 112, 126, 126, 122, 122, 122, 112, 45, 45, 45, 31, 31, 18, 18, 4, 1, 126, 126, 126, 126, 126] 127 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: 550 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054507 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054507 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054507/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054507 Building REAL250005054508 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054508' /scratch/stefan/7922901/working/building/REAL250005054508 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054508 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054508/0 /scratch/stefan/7922901/working/building/REAL250005054508 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/650 `/scratch/stefan/7922901/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)NC=C1) `REAL250005054508.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054508 none CC1=C(C(=O)N(C)CCNC(=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', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 128, 70, 128, 39, 70, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 173, 173, 70, 70, 70, 39, 39, 26, 26, 9, 1, 173, 173, 173] 173 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: 517 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054508 none CC1=C(C(=O)N(C)CCNC(=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', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 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: [1, 1, 1, 1, 7, 7, 23, 23, 64, 88, 167, 169, 167, 173, 173, 173, 173, 173, 1, 1, 1, 2, 2, 2, 23, 23, 23, 64, 64, 88, 88, 169, 173, 1, 1, 1] 173 rigid atoms, others: [0, 1, 2, 3, 35, 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: 635 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054508 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054508 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054508/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054508 Building REAL250005054509 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054509' /scratch/stefan/7922901/working/building/REAL250005054509 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054509 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054509/0 /scratch/stefan/7922901/working/building/REAL250005054509 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/651 `/scratch/stefan/7922901/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=NN1C) `REAL250005054509.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054509 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=NN1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 70, 96, 201, 201, 201, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 70, 70, 96, 96, 201, 201, 1, 2, 2, 2] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 728 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: REAL250005054509 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=NN1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 76, 171, 171, 201, 201, 201, 201, 201, 76, 76, 76, 42, 42, 25, 25, 5, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 614 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054509 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054509 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054509/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054509 Building REAL250005054510 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054510' /scratch/stefan/7922901/working/building/REAL250005054510 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054510 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054510/0 /scratch/stefan/7922901/working/building/REAL250005054510 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/652 `/scratch/stefan/7922901/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1COC(=O)N1) `REAL250005054510.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054510 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1COC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 6, 4, 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: [24, 6, 24, 70, 102, 176, 176, 176, 180, 180, 180, 180, 180, 1, 6, 1, 1, 1, 1, 1, 1, 24, 24, 24, 70, 70, 102, 102, 176, 180, 1, 1, 1, 1] 180 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 693 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: REAL250005054510 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1COC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 6, 4, 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: [92, 44, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 92, 154, 154, 180, 180, 180, 180, 180, 92, 92, 92, 44, 44, 26, 26, 7, 1, 180, 180, 180, 180] 180 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 627 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054510 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054510 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054510/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054510 Building REAL250005054511 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054511' /scratch/stefan/7922901/working/building/REAL250005054511 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054511 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054511/0 /scratch/stefan/7922901/working/building/REAL250005054511 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/653 `/scratch/stefan/7922901/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054511.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054511 none CCCCC(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 175, 117, 67, 117, 48, 67, 33, 48, 21, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 186, 184, 178, 178, 117, 117, 117, 117, 48, 48, 48, 33, 33, 21, 21, 5, 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: 956 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054511 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054511 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054511/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054511 Building REAL250005054512 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054512' /scratch/stefan/7922901/working/building/REAL250005054512 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054512 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054512/0 /scratch/stefan/7922901/working/building/REAL250005054512 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/654 `/scratch/stefan/7922901/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC(C)(C)C1) `REAL250005054512.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054512 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC(C)(C)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 67, 105, 201, 201, 201, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 29, 29, 29, 67, 67, 105, 105, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 39, 40, 13, 15, 16, 17, 18, 19, 20, 30, 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, 33, 34, 35, 36, 37, 38]) total number of confs: 761 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: REAL250005054512 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC(C)(C)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 75, 145, 145, 201, 201, 201, 201, 201, 75, 75, 75, 32, 32, 22, 22, 4, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 683 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054512 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054512 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054512/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054512 Building REAL250005054513 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054513' /scratch/stefan/7922901/working/building/REAL250005054513 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054513 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054513/0 /scratch/stefan/7922901/working/building/REAL250005054513 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/655 `/scratch/stefan/7922901/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054513.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054513 none CC(C)[C@@H](O)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 390 conformations in input total number of sets (complete confs): 390 using faster count positions algorithm for large data unique positions, atoms: [130, 114, 130, 83, 114, 114, 62, 83, 34, 62, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 342, 62, 62, 62, 34, 34, 23, 23, 7, 1] 390 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: 903 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054513 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054513 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054513/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054513 Building REAL250005054514 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054514' /scratch/stefan/7922901/working/building/REAL250005054514 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054514 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054514/0 /scratch/stefan/7922901/working/building/REAL250005054514 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/656 `/scratch/stefan/7922901/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN(C)N=N1) `REAL250005054514.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054514 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN(C)N=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 10, 27, 69, 95, 179, 179, 179, 181, 181, 181, 181, 181, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 69, 69, 95, 95, 179, 181, 1, 2, 2, 2] 181 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) 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: REAL250005054514 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN(C)N=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [85, 44, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 85, 161, 161, 181, 181, 181, 181, 181, 85, 85, 85, 44, 44, 28, 28, 6, 1, 181, 181, 181, 181] 181 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 575 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054514 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054514 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054514/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054514 Building REAL250005054515 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054515' /scratch/stefan/7922901/working/building/REAL250005054515 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054515 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054515/0 /scratch/stefan/7922901/working/building/REAL250005054515 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/657 `/scratch/stefan/7922901/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN(C)C=N1) `REAL250005054515.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054515 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN(C)C=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 40, 83, 109, 201, 201, 201, 201, 201, 201, 201, 201, 1, 12, 1, 1, 1, 1, 1, 1, 40, 40, 40, 83, 83, 109, 109, 201, 201, 2, 2, 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: 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: REAL250005054515 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN(C)C=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 66, 131, 131, 201, 201, 201, 201, 201, 66, 66, 66, 31, 31, 17, 17, 6, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 555 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054515 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054515 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054515/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054515 Building REAL250005054516 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054516' /scratch/stefan/7922901/working/building/REAL250005054516 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054516 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054516/0 /scratch/stefan/7922901/working/building/REAL250005054516 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/658 `/scratch/stefan/7922901/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC1(F)F) `REAL250005054516.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054516 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC1(F)F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 55, 75, 126, 126, 126, 129, 129, 129, 129, 129, 1, 8, 1, 1, 1, 1, 1, 19, 19, 19, 55, 55, 75, 75, 126, 129, 1, 1, 1] 129 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 473 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: REAL250005054516 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC1(F)F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [68, 39, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 68, 106, 106, 129, 129, 129, 129, 68, 68, 68, 39, 39, 25, 25, 8, 1, 129, 129, 129] 129 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 457 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054516 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054516 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054516/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054516 Building REAL250005054517 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054517' /scratch/stefan/7922901/working/building/REAL250005054517 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054517 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054517/0 /scratch/stefan/7922901/working/building/REAL250005054517 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/659 `/scratch/stefan/7922901/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054517.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054517 none CCC(C)=CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 123, 123, 123, 92, 61, 92, 36, 61, 22, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 123, 123, 123, 123, 61, 61, 61, 36, 36, 22, 22, 6, 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: 930 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054517 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054517 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054517/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054517 Building REAL250005054518 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054518' /scratch/stefan/7922901/working/building/REAL250005054518 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054518 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054518/0 /scratch/stefan/7922901/working/building/REAL250005054518 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/660 `/scratch/stefan/7922901/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054518.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054518 none CC(C)C#CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 60, 103, 39, 60, 21, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 103, 103, 60, 60, 60, 39, 39, 21, 21, 7, 1] 103 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: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054518 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054518 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054518/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054518 Building REAL250005054519 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054519' /scratch/stefan/7922901/working/building/REAL250005054519 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054519 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054519/0 /scratch/stefan/7922901/working/building/REAL250005054519 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/661 `/scratch/stefan/7922901/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1(O)CCC1) `REAL250005054519.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054519 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1(O)CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 393 conformations in input total number of sets (complete confs): 393 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 17, 49, 66, 131, 131, 131, 131, 131, 131, 131, 131, 4, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 49, 49, 66, 66, 131, 131, 4, 4, 6, 1, 1, 1, 1, 1, 1] 393 rigid atoms, others: [33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 489 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054519 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1(O)CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 393 conformations in input total number of sets (complete confs): 393 using faster count positions algorithm for large data unique positions, atoms: [67, 33, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 67, 125, 125, 127, 131, 131, 131, 131, 67, 67, 67, 33, 33, 19, 19, 4, 1, 127, 127, 393, 131, 131, 131, 131, 131, 131] 393 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 846 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054519 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054519 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054519/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054519 Building REAL250005054520 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054520' /scratch/stefan/7922901/working/building/REAL250005054520 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054520 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054520/0 /scratch/stefan/7922901/working/building/REAL250005054520 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/662 `/scratch/stefan/7922901/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNN=C1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054520.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054520 none CC1=CNN=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 135, 79, 135, 42, 79, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 79, 79, 79, 42, 42, 24, 24, 7, 1] 193 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: 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: REAL250005054520 none CC1=CNN=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 22, 22, 79, 109, 185, 185, 185, 193, 193, 193, 193, 193, 2, 2, 2, 1, 1, 22, 22, 22, 79, 79, 109, 109, 185, 193] 193 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: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054520 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054520 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054520/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054520 Building REAL250005054521 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054521' /scratch/stefan/7922901/working/building/REAL250005054521 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054521 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054521/0 /scratch/stefan/7922901/working/building/REAL250005054521 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/663 `/scratch/stefan/7922901/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)=C1CCC1) `REAL250005054521.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054521 none CC(C(=O)N(C)CCNC(=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', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 16, 16, 40, 58, 101, 103, 103, 111, 111, 111, 111, 111, 1, 1, 1, 1, 2, 2, 2, 16, 16, 16, 40, 40, 58, 58, 103, 111, 1, 1, 1, 1, 1, 1] 111 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 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: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054521 none CC(C(=O)N(C)CCNC(=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', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 77, 57, 77, 34, 57, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 57, 57, 57, 34, 34, 25, 25, 7, 1, 111, 111, 111, 111, 111, 111] 111 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: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054521 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054521 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054521/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054521 Building REAL250005054522 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054522' /scratch/stefan/7922901/working/building/REAL250005054522 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054522 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054522/0 /scratch/stefan/7922901/working/building/REAL250005054522 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/664 `/scratch/stefan/7922901/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C#CC1CC1) `REAL250005054522.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054522 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C#CC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 6, 30, 60, 139, 139, 139, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 30, 30, 60, 60, 139, 145, 1, 1, 1, 1, 1] 145 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005054522 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C#CC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [75, 42, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 75, 145, 145, 145, 145, 145, 145, 75, 75, 75, 42, 42, 26, 26, 7, 1, 145, 145, 145, 145, 145] 145 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 495 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054522 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054522 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054522/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054522 Building REAL250005054523 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054523' /scratch/stefan/7922901/working/building/REAL250005054523 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054523 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054523/0 /scratch/stefan/7922901/working/building/REAL250005054523 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/665 `/scratch/stefan/7922901/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C#CC(C)(C)C) `REAL250005054523.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054523 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C#CC(C)(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.1', 'C.1', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [82, 48, 28, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 82, 152, 152, 152, 152, 152, 152, 152, 82, 82, 82, 48, 48, 28, 28, 7, 1, 152, 152, 152, 152, 152, 152, 152, 152, 152] 152 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054523 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054523 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054523/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054523 Building REAL250005054524 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054524' /scratch/stefan/7922901/working/building/REAL250005054524 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054524 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054524/0 /scratch/stefan/7922901/working/building/REAL250005054524 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/666 `/scratch/stefan/7922901/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1[N+](=O)[O-]) `REAL250005054524.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054524 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 3, 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: [26, 8, 26, 62, 92, 178, 178, 178, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 62, 62, 92, 92, 178, 201, 1, 1] 201 rigid atoms, others: [32, 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]) total number of confs: 702 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: REAL250005054524 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 3, 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: [83, 41, 25, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 83, 147, 147, 201, 201, 201, 201, 201, 201, 201, 83, 83, 83, 41, 41, 24, 24, 3, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 703 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054524 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054524 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054524/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054524 Building REAL250005054525 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054525' /scratch/stefan/7922901/working/building/REAL250005054525 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054525 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054525/0 /scratch/stefan/7922901/working/building/REAL250005054525 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/667 `/scratch/stefan/7922901/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054525.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054525 none COCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 68, 40, 38, 40, 25, 38, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 68, 68, 38, 38, 38, 25, 25, 16, 16, 4, 1] 81 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: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054525 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054525 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054525/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054525 Building REAL250005054526 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054526' /scratch/stefan/7922901/working/building/REAL250005054526 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054526 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054526/0 /scratch/stefan/7922901/working/building/REAL250005054526 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/668 `/scratch/stefan/7922901/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC1) `REAL250005054526.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054526 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 8, 19, 49, 67, 133, 133, 133, 139, 139, 139, 139, 139, 1, 8, 1, 1, 1, 19, 19, 19, 49, 49, 67, 67, 133, 139, 1, 1, 1, 1, 1] 139 rigid atoms, others: [13, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005054526 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [77, 43, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 75, 109, 109, 139, 139, 77, 77, 77, 43, 43, 28, 28, 7, 1, 139, 139, 139, 139, 139] 139 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 524 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054526 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054526 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054526/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054526 Building REAL250005054527 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054527' /scratch/stefan/7922901/working/building/REAL250005054527 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054527 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054527/0 /scratch/stefan/7922901/working/building/REAL250005054527 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/669 `/scratch/stefan/7922901/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC1) `REAL250005054527.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054527 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 71, 107, 193, 193, 193, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 27, 27, 27, 71, 71, 107, 107, 193, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 747 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: REAL250005054527 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 108, 163, 165, 201, 201, 201, 110, 110, 110, 56, 56, 34, 34, 9, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 715 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054527 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054527 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054527/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054527 Building REAL250005054528 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054528' /scratch/stefan/7922901/working/building/REAL250005054528 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054528 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054528/0 /scratch/stefan/7922901/working/building/REAL250005054528 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/670 `/scratch/stefan/7922901/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCC1) `REAL250005054528.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054528 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 70, 108, 195, 195, 195, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 21, 21, 21, 70, 70, 108, 108, 195, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 759 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054528 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 25, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 88, 167, 169, 201, 201, 201, 201, 90, 90, 90, 44, 44, 25, 25, 6, 1, 200, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 700 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054528 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054528 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054528/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054528 Building REAL250005054529 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054529' /scratch/stefan/7922901/working/building/REAL250005054529 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054529 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054529/0 /scratch/stefan/7922901/working/building/REAL250005054529 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/671 `/scratch/stefan/7922901/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCOCC1) `REAL250005054529.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054529 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 17, 51, 89, 165, 165, 165, 170, 170, 170, 170, 170, 1, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 51, 51, 89, 89, 165, 170, 1, 1, 1, 1, 1, 1, 1, 1, 1] 170 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 661 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054529 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCOCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [78, 37, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 75, 143, 146, 170, 170, 170, 170, 170, 78, 78, 78, 37, 37, 20, 20, 7, 1, 170, 170, 170, 170, 170, 170, 170, 170, 170] 170 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 594 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054529 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054529 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054529/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054529 Building REAL250005054530 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054530' /scratch/stefan/7922901/working/building/REAL250005054530 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054530 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054530/0 /scratch/stefan/7922901/working/building/REAL250005054530 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/672 `/scratch/stefan/7922901/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN(C)N=C1) `REAL250005054530.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054530 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN(C)N=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 31, 70, 102, 195, 195, 195, 201, 201, 201, 201, 201, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 31, 70, 70, 102, 102, 195, 201, 2, 2, 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: 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: REAL250005054530 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN(C)N=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 52, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 109, 187, 187, 201, 201, 201, 201, 201, 109, 109, 109, 52, 52, 32, 32, 9, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 651 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054530 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054530 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054530/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054530 Building REAL250005054531 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054531' /scratch/stefan/7922901/working/building/REAL250005054531 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054531 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054531/0 /scratch/stefan/7922901/working/building/REAL250005054531 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/673 `/scratch/stefan/7922901/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005054531.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054531 none CCC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 5, 5, 5, 5, 5, 5, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 8, 8, 8, 8, 8, 7, 5, 5, 5, 5, 5, 5, 5, 3, 1, 9, 9, 9, 9, 9, 9] 9 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: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054531 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054531 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054531/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054531 Building REAL250005054532 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054532' /scratch/stefan/7922901/working/building/REAL250005054532 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054532 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054532/0 /scratch/stefan/7922901/working/building/REAL250005054532 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/674 `/scratch/stefan/7922901/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1COC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054532.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054532 none CC1COC(C(=O)N(C)CCNC(=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', '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, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 72, 56, 72, 30, 56, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 78, 56, 56, 56, 30, 30, 18, 18, 6, 1, 78, 78] 78 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: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054532 none CC1COC(C(=O)N(C)CCNC(=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', '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, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 16, 16, 36, 48, 75, 75, 75, 78, 78, 78, 78, 78, 1, 2, 2, 2, 1, 1, 1, 1, 16, 16, 16, 36, 36, 48, 48, 75, 78, 1, 1] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 24, 25, 26, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054532 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054532 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054532/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054532 Building REAL250005054533 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054533' /scratch/stefan/7922901/working/building/REAL250005054533 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054533 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054533/0 /scratch/stefan/7922901/working/building/REAL250005054533 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/675 `/scratch/stefan/7922901/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@]12C[C@H]1CCC2) `REAL250005054533.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054533 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@]12C[C@H]1CCC2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 21, 35, 69, 69, 69, 72, 72, 72, 72, 72, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 35, 35, 69, 72, 1, 1, 1, 1, 1, 1, 1, 1] 72 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054533 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@]12C[C@H]1CCC2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [48, 27, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 48, 72, 72, 72, 72, 72, 72, 72, 72, 48, 48, 48, 27, 27, 17, 17, 6, 1, 72, 72, 72, 72, 72, 72, 72, 72] 72 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 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: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054533 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054533 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054533/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054533 Building REAL250005054534 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054534' /scratch/stefan/7922901/working/building/REAL250005054534 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054534 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054534/0 /scratch/stefan/7922901/working/building/REAL250005054534 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/676 `/scratch/stefan/7922901/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCC(=O)N1) `REAL250005054534.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054534 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 4, 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: [25, 7, 25, 72, 108, 190, 190, 190, 194, 194, 194, 194, 194, 1, 7, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 72, 72, 108, 108, 190, 194, 1, 1, 1, 1, 1] 194 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 758 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: REAL250005054534 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 4, 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: [94, 46, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 92, 168, 168, 194, 194, 194, 194, 194, 194, 94, 94, 94, 46, 46, 28, 28, 8, 1, 194, 194, 194, 194, 194] 194 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 665 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054534 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054534 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054534/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054534 Building REAL250005054535 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054535' /scratch/stefan/7922901/working/building/REAL250005054535 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054535 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054535/0 /scratch/stefan/7922901/working/building/REAL250005054535 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/677 `/scratch/stefan/7922901/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@H+](C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054535.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054535 none CCC[N@H+](C)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 16, 16, 16, 16, 16, 13, 16, 13, 13, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 17, 17, 16, 16, 16, 16, 16, 13, 13, 13, 13, 13, 11, 11, 4, 1] 21 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: 93 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054535 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054535/1 /scratch/stefan/7922901/working/building/REAL250005054535 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/678 `/scratch/stefan/7922901/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@@H+](C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054535.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005054535 none CCC[N@@H+](C)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 18, 17, 17, 17, 17, 17, 14, 17, 14, 14, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 18, 18, 17, 17, 17, 17, 17, 14, 14, 14, 14, 14, 13, 13, 5, 1] 22 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: 92 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054535 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054535 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054535/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054535/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054535 Building REAL250005054536 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054536' /scratch/stefan/7922901/working/building/REAL250005054536 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054536 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054536/0 /scratch/stefan/7922901/working/building/REAL250005054536 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/679 `/scratch/stefan/7922901/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC(C)(C)C) `REAL250005054536.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054536 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC(C)(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [59, 29, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 59, 125, 125, 176, 176, 177, 177, 177, 59, 59, 59, 29, 29, 20, 20, 4, 1, 177, 177, 177, 177, 177, 177, 177, 177, 177, 177, 177, 177, 177] 177 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 685 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054536 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054536 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054536/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054536 Building REAL250005054537 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054537' /scratch/stefan/7922901/working/building/REAL250005054537 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054537 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054537/0 /scratch/stefan/7922901/working/building/REAL250005054537 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/680 `/scratch/stefan/7922901/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NC=N1) `REAL250005054537.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054537 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 61, 95, 183, 183, 183, 198, 198, 198, 198, 198, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21, 61, 61, 95, 95, 183, 198, 1, 1, 1] 198 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 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]) 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: REAL250005054537 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [110, 53, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 110, 186, 186, 198, 198, 198, 198, 198, 110, 110, 110, 53, 53, 34, 34, 11, 1, 198, 198, 198] 198 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 647 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054537 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054537 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054537/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054537 Building REAL250005054538 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054538' /scratch/stefan/7922901/working/building/REAL250005054538 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054538 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054538/0 /scratch/stefan/7922901/working/building/REAL250005054538 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/681 `/scratch/stefan/7922901/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CC=CO1) `REAL250005054538.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054538 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CC=CO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 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: [47, 21, 47, 98, 132, 201, 201, 201, 201, 201, 201, 201, 201, 4, 21, 1, 1, 1, 1, 1, 1, 47, 47, 47, 98, 98, 132, 132, 201, 201, 4, 4, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 784 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054538 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CC=CO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 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: [54, 26, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 54, 97, 97, 167, 201, 201, 201, 201, 54, 54, 54, 26, 26, 14, 14, 4, 1, 167, 167, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 731 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054538 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054538 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054538/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054538 Building REAL250005054539 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054539' /scratch/stefan/7922901/working/building/REAL250005054539 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054539 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054539/0 /scratch/stefan/7922901/working/building/REAL250005054539 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/682 `/scratch/stefan/7922901/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC=CC=N1) `REAL250005054539.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054539 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC=CC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 3, 7, 7, 7, 3, 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: [31, 11, 31, 74, 90, 171, 171, 171, 187, 187, 187, 187, 187, 1, 11, 1, 1, 1, 1, 1, 1, 31, 31, 31, 74, 74, 90, 90, 171, 187, 1, 1, 1] 187 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 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]) 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: REAL250005054539 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC=CC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 3, 7, 7, 7, 3, 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: [98, 51, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 96, 175, 177, 187, 187, 177, 187, 187, 98, 98, 98, 51, 51, 34, 34, 11, 1, 187, 177, 187] 187 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 644 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054539 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054539 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054539/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054539 Building REAL250005054540 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054540' /scratch/stefan/7922901/working/building/REAL250005054540 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054540 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054540/0 /scratch/stefan/7922901/working/building/REAL250005054540 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/683 `/scratch/stefan/7922901/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054540.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054540 none CCC(C)CCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 127, 191, 107, 43, 41, 43, 32, 41, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 195, 195, 191, 195, 134, 134, 108, 108, 41, 41, 41, 32, 32, 20, 20, 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: 1015 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054540 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054540 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054540/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054540 Building REAL250005054541 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054541' /scratch/stefan/7922901/working/building/REAL250005054541 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054541 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054541/0 /scratch/stefan/7922901/working/building/REAL250005054541 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/684 `/scratch/stefan/7922901/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CN=N1) `REAL250005054541.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054541 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CN=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 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: [21, 9, 21, 57, 85, 171, 171, 171, 177, 177, 177, 177, 177, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 57, 57, 85, 85, 171, 177, 1, 1, 1] 177 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 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]) 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: REAL250005054541 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=CN=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 3, 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: [101, 52, 36, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 101, 166, 166, 177, 177, 177, 177, 174, 101, 101, 101, 52, 52, 36, 36, 9, 1, 177, 177, 177] 177 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 580 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054541 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054541 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054541/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054541 Building REAL250005054542 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054542' /scratch/stefan/7922901/working/building/REAL250005054542 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054542 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054542/0 /scratch/stefan/7922901/working/building/REAL250005054542 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/685 `/scratch/stefan/7922901/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OCCC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054542.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054542 none CC1OCCC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 76, 50, 76, 31, 50, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 81, 81, 50, 50, 50, 31, 31, 19, 19, 7, 1] 81 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: 292 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: REAL250005054542 none CC1OCCC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 13, 13, 36, 50, 79, 79, 79, 81, 81, 81, 81, 81, 2, 2, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 36, 36, 50, 50, 79, 81] 81 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: 305 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054542 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054542 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054542/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054542 Building REAL250005054543 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054543' /scratch/stefan/7922901/working/building/REAL250005054543 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054543 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054543/0 /scratch/stefan/7922901/working/building/REAL250005054543 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/686 `/scratch/stefan/7922901/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CCOC1) `REAL250005054543.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054543 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CCOC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 3, 6, 18, 31, 77, 77, 77, 79, 79, 79, 79, 79, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 31, 31, 77, 79, 2, 2, 2, 1, 1, 1, 1, 1, 1] 79 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 278 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054543 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CCOC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [52, 33, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 52, 79, 79, 79, 79, 79, 79, 79, 52, 52, 52, 33, 33, 21, 21, 6, 1, 79, 79, 79, 79, 79, 79, 79, 79, 79] 79 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 288 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054543 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054543 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054543/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054543 Building REAL250005054544 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054544' /scratch/stefan/7922901/working/building/REAL250005054544 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054544 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054544/0 /scratch/stefan/7922901/working/building/REAL250005054544 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/687 `/scratch/stefan/7922901/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054544.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054544 none CCC(CC)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 183, 142, 183, 196, 51, 49, 51, 31, 49, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 196, 196, 196, 196, 196, 183, 196, 196, 196, 196, 196, 143, 143, 49, 49, 49, 31, 31, 18, 18, 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: 949 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054544 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054544 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054544/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054544 Building REAL250005054545 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054545' /scratch/stefan/7922901/working/building/REAL250005054545 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054545 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054545/0 /scratch/stefan/7922901/working/building/REAL250005054545 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/688 `/scratch/stefan/7922901/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054545.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054545 none CCC(C)C(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 123, 107, 123, 77, 107, 64, 77, 38, 64, 23, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 123, 123, 123, 123, 107, 107, 107, 107, 64, 64, 64, 38, 38, 23, 23, 6, 1] 125 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: 539 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054545 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054545 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054545/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054545 Building REAL250005054546 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054546' /scratch/stefan/7922901/working/building/REAL250005054546 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054546 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054546/0 /scratch/stefan/7922901/working/building/REAL250005054546 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/689 `/scratch/stefan/7922901/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054546.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054546 none CCCC(CC)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [160, 153, 114, 69, 113, 120, 62, 69, 32, 62, 19, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 160, 160, 160, 157, 160, 158, 158, 114, 139, 139, 139, 139, 139, 62, 62, 62, 32, 32, 19, 19, 4, 1] 161 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: 1033 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054546 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054546 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054546/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054546 Building REAL250005054547 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054547' /scratch/stefan/7922901/working/building/REAL250005054547 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054547 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054547/0 /scratch/stefan/7922901/working/building/REAL250005054547 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/690 `/scratch/stefan/7922901/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)CC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054547.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054547 none CCC1(C)CC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 135, 135, 135, 135, 116, 72, 116, 40, 72, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 149, 135, 135, 135, 135, 135, 135, 72, 72, 72, 40, 40, 25, 25, 9, 1] 149 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: 565 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: REAL250005054547 none CCC1(C)CC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 46, 65, 124, 124, 124, 135, 135, 135, 135, 135, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 15, 15, 15, 46, 46, 65, 65, 124, 135] 149 rigid atoms, others: [1, 2, 3, 4, 5, 6, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 483 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054547 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054547 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054547/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054547 Building REAL250005054548 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054548' /scratch/stefan/7922901/working/building/REAL250005054548 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054548 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054548/0 /scratch/stefan/7922901/working/building/REAL250005054548 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/691 `/scratch/stefan/7922901/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054548.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054548 none COCC(C)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 81, 53, 81, 23, 22, 23, 20, 22, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 81, 81, 81, 81, 53, 53, 22, 22, 22, 20, 20, 14, 14, 4, 1] 104 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: 499 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054548 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054548 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054548/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054548 Building REAL250005054549 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054549' /scratch/stefan/7922901/working/building/REAL250005054549 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054549 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054549/0 /scratch/stefan/7922901/working/building/REAL250005054549 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/692 `/scratch/stefan/7922901/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC(F)C1) `REAL250005054549.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054549 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC(F)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 6, 22, 67, 102, 177, 177, 177, 180, 180, 180, 180, 180, 1, 6, 1, 1, 1, 1, 1, 1, 22, 22, 22, 67, 67, 102, 102, 177, 180, 1, 1, 1, 1, 1, 1, 1, 1] 180 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 715 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054549 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC(F)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [83, 40, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 81, 156, 156, 180, 180, 180, 180, 180, 83, 83, 83, 40, 40, 23, 23, 8, 1, 180, 180, 180, 180, 180, 180, 180, 180] 180 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 621 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054549 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054549 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054549/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054549 Building REAL250005054550 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054550' /scratch/stefan/7922901/working/building/REAL250005054550 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054550 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054550/0 /scratch/stefan/7922901/working/building/REAL250005054550 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/693 `/scratch/stefan/7922901/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC1(C)CC1) `REAL250005054550.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054550 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC1(C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 39, 78, 102, 201, 201, 201, 201, 201, 201, 201, 201, 8, 19, 7, 1, 1, 1, 1, 1, 40, 40, 40, 78, 78, 102, 102, 201, 201, 8, 8, 7, 7, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 731 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: REAL250005054550 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC1(C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 68, 112, 112, 119, 120, 201, 201, 201, 68, 68, 68, 36, 36, 23, 23, 4, 1, 119, 119, 120, 120, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 748 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054550 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054550 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054550/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054550 Building REAL250005054551 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054551' /scratch/stefan/7922901/working/building/REAL250005054551 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054551 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054551/0 /scratch/stefan/7922901/working/building/REAL250005054551 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/694 `/scratch/stefan/7922901/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)ON=C1) `REAL250005054551.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054551 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 142, 84, 142, 44, 84, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 84, 84, 84, 44, 44, 28, 28, 7, 1, 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]) 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: REAL250005054551 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 8, 8, 24, 24, 75, 113, 197, 197, 197, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 24, 24, 24, 75, 75, 113, 113, 197, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 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: 765 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054551 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054551 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054551/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054551 Building REAL250005054552 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054552' /scratch/stefan/7922901/working/building/REAL250005054552 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054552 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054552/0 /scratch/stefan/7922901/working/building/REAL250005054552 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/695 `/scratch/stefan/7922901/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054552.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054552 none CC[N@H+](C)CCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 14, 14, 9, 9, 9, 9, 9, 9, 9, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1] 14 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: 61 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054552 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054552/1 /scratch/stefan/7922901/working/building/REAL250005054552 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/696 `/scratch/stefan/7922901/working/3D/696' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054552.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005054552 none CC[N@@H+](C)CCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 15, 15, 10, 10, 10, 10, 10, 10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1] 15 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: 64 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054552 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054552 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054552/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054552/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054552 Building REAL250005054553 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054553' /scratch/stefan/7922901/working/building/REAL250005054553 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054553 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054553/0 /scratch/stefan/7922901/working/building/REAL250005054553 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/697 `/scratch/stefan/7922901/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CON=C1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054553.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054553 none CC1=CON=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 150, 86, 150, 37, 86, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 86, 86, 86, 37, 37, 25, 25, 5, 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: 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: REAL250005054553 none CC1=CON=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 23, 23, 78, 116, 194, 194, 194, 201, 201, 201, 201, 201, 2, 2, 2, 1, 23, 23, 23, 78, 78, 116, 116, 194, 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: 765 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054553 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054553 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054553/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054553 Building REAL250005054554 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054554' /scratch/stefan/7922901/working/building/REAL250005054554 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054554 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054554/0 /scratch/stefan/7922901/working/building/REAL250005054554 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/698 `/scratch/stefan/7922901/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1N=CN=N1) `REAL250005054554.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054554 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1N=CN=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [52, 35, 52, 94, 116, 187, 187, 187, 187, 187, 187, 187, 187, 8, 35, 1, 1, 1, 1, 1, 1, 52, 52, 52, 94, 94, 116, 116, 187, 187, 8, 8, 1] 187 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 681 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: REAL250005054554 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1N=CN=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [53, 29, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 53, 96, 96, 114, 187, 187, 187, 187, 53, 53, 53, 29, 29, 18, 18, 4, 1, 114, 114, 187] 187 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 562 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054554 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054554 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054554/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054554 Building REAL250005054555 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054555' /scratch/stefan/7922901/working/building/REAL250005054555 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054555 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054555/0 /scratch/stefan/7922901/working/building/REAL250005054555 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/699 `/scratch/stefan/7922901/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054555.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054555 none CCCC[C@@H](C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 175, 116, 65, 116, 116, 48, 65, 33, 48, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 184, 186, 178, 178, 116, 116, 116, 48, 48, 48, 33, 33, 21, 21, 5, 1] 201 rigid atoms, others: [42, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 957 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054555 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054555 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054555/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054555 Building REAL250005054556 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054556' /scratch/stefan/7922901/working/building/REAL250005054556 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054556 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054556/0 /scratch/stefan/7922901/working/building/REAL250005054556 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/700 `/scratch/stefan/7922901/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054556.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054556 none CCC(C)(C)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [112, 96, 46, 96, 96, 28, 28, 28, 24, 28, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 112, 116, 116, 116, 116, 96, 96, 96, 96, 96, 96, 46, 46, 28, 28, 28, 24, 24, 14, 14, 4, 1] 116 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: 578 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054556 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054556 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054556/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054556 Building REAL250005054557 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054557' /scratch/stefan/7922901/working/building/REAL250005054557 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054557 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054557/0 /scratch/stefan/7922901/working/building/REAL250005054557 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/701 `/scratch/stefan/7922901/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054557.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054557 none CC(C)C(C)(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 27, 39, 19, 27, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 27, 27, 27, 19, 19, 12, 12, 4, 1] 39 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: 162 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054557 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054557 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054557/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054557 Building REAL250005054558 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054558' /scratch/stefan/7922901/working/building/REAL250005054558 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054558 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054558/0 /scratch/stefan/7922901/working/building/REAL250005054558 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/702 `/scratch/stefan/7922901/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054558.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054558 none C=CC(C)(C)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 101, 161, 161, 55, 49, 55, 33, 49, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 165, 165, 165, 101, 101, 49, 49, 49, 33, 33, 22, 22, 4, 1] 165 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: 792 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054558 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054558 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054558/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054558 Building REAL250005054559 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054559' /scratch/stefan/7922901/working/building/REAL250005054559 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054559 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054559/0 /scratch/stefan/7922901/working/building/REAL250005054559 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/703 `/scratch/stefan/7922901/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1N=CC=N1) `REAL250005054559.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054559 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1N=CC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [24, 16, 24, 46, 54, 100, 100, 100, 100, 100, 100, 100, 100, 5, 16, 1, 1, 1, 1, 1, 1, 25, 25, 25, 46, 46, 54, 54, 100, 100, 5, 5, 1, 1] 100 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 372 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054559 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1N=CC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [62, 28, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 62, 116, 116, 181, 187, 187, 187, 187, 62, 62, 62, 28, 28, 14, 14, 4, 1, 181, 181, 187, 187] 187 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 727 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054559 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054559 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054559/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054559 Building REAL250005054560 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054560' /scratch/stefan/7922901/working/building/REAL250005054560 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054560 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054560/0 /scratch/stefan/7922901/working/building/REAL250005054560 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/704 `/scratch/stefan/7922901/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054560.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054560 none C=CCCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 111, 95, 33, 31, 33, 25, 31, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 194, 194, 126, 126, 96, 96, 31, 31, 31, 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: 981 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054560 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054560 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054560/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054560 Building REAL250005054561 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054561' /scratch/stefan/7922901/working/building/REAL250005054561 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054561 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054561/0 /scratch/stefan/7922901/working/building/REAL250005054561 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/705 `/scratch/stefan/7922901/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054561.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054561 none CCC(C)(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 85, 69, 85, 85, 55, 69, 36, 55, 25, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 85, 85, 85, 85, 85, 85, 55, 55, 55, 36, 36, 25, 25, 9, 1] 109 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: 501 number of broken/clashed sets: 109 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054561 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054561 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054561/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054561 Building REAL250005054562 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054562' /scratch/stefan/7922901/working/building/REAL250005054562 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054562 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054562/0 /scratch/stefan/7922901/working/building/REAL250005054562 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/706 `/scratch/stefan/7922901/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054562.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054562 none CCCC(C)(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 41, 57, 24, 41, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 41, 41, 41, 24, 24, 15, 15, 4, 1] 57 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: 229 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054562 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054562 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054562/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054562 Building REAL250005054563 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054563' /scratch/stefan/7922901/working/building/REAL250005054563 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054563 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054563/0 /scratch/stefan/7922901/working/building/REAL250005054563 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/707 `/scratch/stefan/7922901/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C(N)=O)CC1) `REAL250005054563.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054563 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C(N)=O)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 39, 72, 169, 169, 169, 185, 185, 185, 185, 185, 1, 4, 1, 1, 7, 7, 1, 1, 11, 11, 11, 39, 39, 72, 72, 169, 185, 7, 7, 1, 1, 1, 1] 200 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 638 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: REAL250005054563 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C(N)=O)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.am', 'O.2', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [90, 50, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 90, 170, 170, 185, 200, 200, 185, 185, 90, 90, 90, 50, 50, 31, 31, 9, 1, 200, 200, 185, 185, 185, 185] 200 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 690 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054563 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054563 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054563/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054563 Building REAL250005054564 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054564' /scratch/stefan/7922901/working/building/REAL250005054564 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054564 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054564/0 /scratch/stefan/7922901/working/building/REAL250005054564 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/708 `/scratch/stefan/7922901/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(N)=O) `REAL250005054564.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054564 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(N)=O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [75, 41, 29, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 75, 101, 101, 121, 121, 75, 75, 75, 41, 41, 29, 29, 9, 1, 121, 121] 121 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 26] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28]) total number of confs: 459 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054564 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054564 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054564/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054564 Building REAL250005054565 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054565' /scratch/stefan/7922901/working/building/REAL250005054565 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054565 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054565/0 /scratch/stefan/7922901/working/building/REAL250005054565 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/709 `/scratch/stefan/7922901/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC=C1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054565.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054565 none CC1=NOC=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 139, 75, 139, 40, 75, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 75, 75, 75, 40, 40, 24, 24, 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: 569 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: REAL250005054565 none CC1=NOC=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 73, 110, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 27, 27, 27, 73, 73, 110, 110, 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: 773 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054565 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054565 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054565/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054565 Building REAL250005054566 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054566' /scratch/stefan/7922901/working/building/REAL250005054566 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054566 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054566/0 /scratch/stefan/7922901/working/building/REAL250005054566 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/710 `/scratch/stefan/7922901/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CC=CC1) `REAL250005054566.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054566 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CC=CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 9, 15, 34, 34, 34, 36, 36, 36, 36, 36, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 15, 15, 34, 36, 2, 2, 2, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 129 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: REAL250005054566 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CC=CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [35, 23, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 35, 36, 36, 36, 36, 36, 36, 36, 35, 35, 35, 23, 23, 16, 16, 6, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36] 36 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054566 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054566 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054566/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054566 Building REAL250005054567 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054567' /scratch/stefan/7922901/working/building/REAL250005054567 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054567 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054567/0 /scratch/stefan/7922901/working/building/REAL250005054567 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/711 `/scratch/stefan/7922901/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005054567.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054567 none COC(C(=O)N(C)CCNC(=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', '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, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [44, 43, 29, 19, 29, 17, 19, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 43, 46, 46, 44, 44, 44, 43, 19, 19, 19, 17, 17, 13, 13, 4, 1, 46, 46, 46, 46, 46, 46, 46] 46 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: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054567 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054567 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054567/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054567 Building REAL250005054568 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054568' /scratch/stefan/7922901/working/building/REAL250005054568 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054568 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054568/0 /scratch/stefan/7922901/working/building/REAL250005054568 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/712 `/scratch/stefan/7922901/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054568.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054568 none CC1CC1CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 173, 72, 69, 72, 39, 69, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 174, 174, 69, 69, 69, 39, 39, 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: 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: REAL250005054568 none CC1CC1CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 26, 26, 78, 103, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 5, 5, 26, 26, 26, 78, 78, 103, 103, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054568 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054568 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054568/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054568 Building REAL250005054569 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054569' /scratch/stefan/7922901/working/building/REAL250005054569 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054569 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054569/0 /scratch/stefan/7922901/working/building/REAL250005054569 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/713 `/scratch/stefan/7922901/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(CC)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054569.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054569 none C=CC(C)(CC)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [36, 32, 32, 32, 32, 43, 27, 32, 18, 27, 11, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 36, 36, 36, 32, 32, 32, 43, 43, 43, 43, 43, 27, 27, 27, 18, 18, 11, 11, 3, 1] 43 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: 209 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054569 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054569 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054569/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054569 Building REAL250005054570 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054570' /scratch/stefan/7922901/working/building/REAL250005054570 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054570 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054570/0 /scratch/stefan/7922901/working/building/REAL250005054570 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/714 `/scratch/stefan/7922901/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C[C@H]1CCOC1) `REAL250005054570.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054570 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 18, 40, 81, 104, 201, 201, 201, 201, 201, 201, 201, 201, 5, 18, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 81, 81, 104, 104, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 717 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: REAL250005054570 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 30, 20, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 60, 115, 115, 137, 201, 201, 201, 201, 201, 60, 60, 60, 30, 30, 19, 19, 3, 1, 137, 137, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 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: 767 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054570 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054570 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054570/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054570 Building REAL250005054571 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054571' /scratch/stefan/7922901/working/building/REAL250005054571 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054571 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054571/0 /scratch/stefan/7922901/working/building/REAL250005054571 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/715 `/scratch/stefan/7922901/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054571.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054571 none CCC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 37, 53, 26, 37, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 37, 37, 37, 26, 26, 17, 17, 7, 1, 53, 53, 53, 53] 53 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: 197 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: REAL250005054571 none CCC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 3, 3, 6, 6, 14, 23, 50, 50, 50, 53, 53, 53, 53, 53, 1, 1, 3, 3, 3, 3, 3, 6, 6, 6, 14, 14, 23, 23, 50, 53, 1, 1, 1, 1] 53 rigid atoms, others: [1, 2, 3, 36, 37, 35, 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, 32, 33]) total number of confs: 206 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054571 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054571 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054571/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054571 Building REAL250005054572 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054572' /scratch/stefan/7922901/working/building/REAL250005054572 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054572 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054572/0 /scratch/stefan/7922901/working/building/REAL250005054572 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/716 `/scratch/stefan/7922901/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)C) `REAL250005054572.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054572 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 27, 19, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 37, 40, 40, 40, 40, 40, 37, 37, 37, 27, 27, 19, 19, 7, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40] 40 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 150 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054572 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054572 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054572/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054572 Building REAL250005054573 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054573' /scratch/stefan/7922901/working/building/REAL250005054573 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054573 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054573/0 /scratch/stefan/7922901/working/building/REAL250005054573 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/717 `/scratch/stefan/7922901/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NN=CN1) `REAL250005054573.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054573 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NN=CN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [23, 14, 23, 55, 67, 121, 121, 121, 121, 121, 121, 121, 121, 6, 14, 1, 1, 1, 1, 1, 1, 23, 23, 23, 55, 55, 67, 67, 121, 121, 6, 6, 1, 1] 121 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 465 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: REAL250005054573 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NN=CN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [49, 19, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 91, 91, 121, 121, 121, 121, 121, 49, 49, 49, 19, 19, 8, 8, 2, 1, 121, 121, 121, 121] 121 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 486 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054573 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054573/1 /scratch/stefan/7922901/working/building/REAL250005054573 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/718 `/scratch/stefan/7922901/working/3D/718' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NC=NN1) `REAL250005054573.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054573 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NC=NN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 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: [39, 22, 39, 97, 119, 201, 201, 201, 201, 201, 201, 201, 201, 6, 22, 1, 1, 1, 1, 1, 1, 39, 39, 39, 97, 97, 119, 119, 201, 201, 6, 6, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 743 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054573 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NC=NN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 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: [71, 37, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 71, 149, 149, 187, 201, 201, 201, 201, 71, 71, 71, 37, 37, 24, 24, 4, 1, 187, 187, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 698 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054573 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054573 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054573/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054573/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054573 Building REAL250005054574 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054574' /scratch/stefan/7922901/working/building/REAL250005054574 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054574 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054574/0 /scratch/stefan/7922901/working/building/REAL250005054574 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/719 `/scratch/stefan/7922901/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054574.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054574 none C=C(C)CCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 123, 71, 55, 71, 29, 55, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 145, 145, 145, 124, 124, 55, 55, 55, 29, 29, 18, 18, 4, 1] 145 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: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054574 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054574 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054574/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054574 Building REAL250005054575 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054575' /scratch/stefan/7922901/working/building/REAL250005054575 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054575 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054575/0 /scratch/stefan/7922901/working/building/REAL250005054575 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/720 `/scratch/stefan/7922901/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NS1) `REAL250005054575.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054575 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 27, 71, 104, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 27, 27, 27, 71, 71, 104, 104, 201, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 750 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: REAL250005054575 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 76, 148, 148, 201, 201, 201, 201, 76, 76, 76, 40, 40, 22, 22, 6, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 615 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054575 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054575 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054575/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054575 Building REAL250005054576 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054576' /scratch/stefan/7922901/working/building/REAL250005054576 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054576 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054576/0 /scratch/stefan/7922901/working/building/REAL250005054576 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/721 `/scratch/stefan/7922901/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(C)(F)F) `REAL250005054576.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054576 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(C)(F)F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 55, 105, 105, 127, 201, 201, 201, 55, 55, 55, 25, 25, 14, 14, 4, 1, 127, 127, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 869 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054576 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054576 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054576/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054576 Building REAL250005054577 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054577' /scratch/stefan/7922901/working/building/REAL250005054577 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054577 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054577/0 /scratch/stefan/7922901/working/building/REAL250005054577 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/722 `/scratch/stefan/7922901/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054577.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054577 none CCCC1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 68, 65, 62, 37, 62, 24, 37, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 65, 69, 69, 69, 69, 69, 68, 68, 37, 37, 37, 24, 24, 13, 13, 4, 1, 65, 65, 65, 65] 69 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: 259 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: REAL250005054577 none CCCC1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 1, 1, 1, 3, 3, 8, 8, 20, 30, 60, 60, 60, 65, 65, 65, 65, 65, 1, 1, 10, 10, 10, 10, 10, 7, 7, 8, 8, 8, 20, 20, 30, 30, 60, 65, 1, 1, 1, 1] 69 rigid atoms, others: [2, 3, 4, 37, 38, 39, 40, 19, 20] 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, 35, 36]) total number of confs: 281 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054577 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054577 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054577/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054577 Building REAL250005054578 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054578' /scratch/stefan/7922901/working/building/REAL250005054578 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054578 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054578/0 /scratch/stefan/7922901/working/building/REAL250005054578 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/723 `/scratch/stefan/7922901/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1C[C@H]1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054578.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054578 none CCC[C@@H]1C[C@H]1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 134, 134, 134, 134, 62, 134, 51, 62, 31, 51, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 134, 134, 51, 51, 51, 31, 31, 19, 19, 4, 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: 844 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: REAL250005054578 none CCC[C@@H]1C[C@H]1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 20, 20, 45, 63, 118, 118, 118, 134, 134, 134, 134, 134, 13, 13, 13, 13, 13, 7, 7, 1, 1, 20, 20, 20, 45, 45, 63, 63, 118, 134] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 514 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054578 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054578 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054578/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054578 Building REAL250005054579 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054579' /scratch/stefan/7922901/working/building/REAL250005054579 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054579 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054579/0 /scratch/stefan/7922901/working/building/REAL250005054579 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/724 `/scratch/stefan/7922901/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054579.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054579 none CC(C)C1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 2, 1, 5, 5, 5, 5] 5 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: 19 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: REAL250005054579 none CC(C)C1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 5 rigid atoms, others: [1, 3, 4, 37, 38, 39, 40, 19, 20] set([0, 2, 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, 35, 36]) total number of confs: 28 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054579 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054579 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054579/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054579 Building REAL250005054580 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054580' /scratch/stefan/7922901/working/building/REAL250005054580 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054580 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054580/0 /scratch/stefan/7922901/working/building/REAL250005054580 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/725 `/scratch/stefan/7922901/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C)(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054580.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054580 none C=C1CC(C)(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 67, 94, 40, 67, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 94, 67, 67, 67, 40, 40, 26, 26, 9, 1, 94, 94] 94 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: 348 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054580 none C=C1CC(C)(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 8, 8, 24, 41, 91, 91, 91, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 24, 24, 41, 41, 91, 94, 1, 1] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 23, 24, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 342 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054580 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054580 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054580/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054580 Building REAL250005054581 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054581' /scratch/stefan/7922901/working/building/REAL250005054581 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054581 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054581/0 /scratch/stefan/7922901/working/building/REAL250005054581 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/726 `/scratch/stefan/7922901/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CF)CC1) `REAL250005054581.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054581 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CF)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'F', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 3, 8, 29, 49, 136, 136, 136, 157, 157, 157, 157, 157, 1, 3, 1, 1, 10, 1, 1, 8, 8, 8, 29, 29, 49, 49, 136, 157, 10, 10, 1, 1, 1, 1] 167 rigid atoms, others: [32, 33, 34, 13, 15, 16, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 521 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: REAL250005054581 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CF)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'F', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [93, 44, 27, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 93, 148, 148, 157, 167, 157, 157, 93, 93, 93, 44, 44, 27, 27, 6, 1, 167, 167, 157, 157, 157, 157] 167 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 605 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054581 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054581 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054581/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054581 Building REAL250005054582 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054582' /scratch/stefan/7922901/working/building/REAL250005054582 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054582 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054582/0 /scratch/stefan/7922901/working/building/REAL250005054582 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/727 `/scratch/stefan/7922901/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC2(CC2)C1) `REAL250005054582.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054582 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC2(CC2)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 64, 106, 201, 201, 201, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 27, 27, 27, 64, 64, 106, 106, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 757 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: REAL250005054582 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC2(CC2)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 73, 147, 147, 201, 201, 201, 201, 201, 73, 73, 73, 32, 32, 21, 21, 4, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 688 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054582 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054582 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054582/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054582 Building REAL250005054583 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054583' /scratch/stefan/7922901/working/building/REAL250005054583 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054583 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054583/0 /scratch/stefan/7922901/working/building/REAL250005054583 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/728 `/scratch/stefan/7922901/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054583.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054583 none CCCCCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 181, 152, 121, 109, 47, 35, 47, 25, 35, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 195, 201, 201, 199, 199, 189, 189, 149, 149, 126, 126, 110, 110, 35, 35, 35, 25, 25, 16, 16, 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: 995 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054583 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054583 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054583/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054583 Building REAL250005054584 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054584' /scratch/stefan/7922901/working/building/REAL250005054584 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054584 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054584/0 /scratch/stefan/7922901/working/building/REAL250005054584 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/729 `/scratch/stefan/7922901/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054584.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054584 none CC(C)C(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 87, 91, 69, 87, 54, 69, 32, 54, 23, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 91, 91, 87, 87, 87, 87, 54, 54, 54, 32, 32, 23, 23, 8, 1] 91 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: 381 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054584 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054584 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054584/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054584 Building REAL250005054585 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054585' /scratch/stefan/7922901/working/building/REAL250005054585 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054585 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054585/0 /scratch/stefan/7922901/working/building/REAL250005054585 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/730 `/scratch/stefan/7922901/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054585.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054585 none CC1CCC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 82, 55, 82, 32, 55, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 55, 55, 55, 32, 32, 22, 22, 6, 1, 112, 112] 112 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: 412 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: REAL250005054585 none CC1CCC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 37, 55, 108, 108, 108, 112, 112, 112, 112, 112, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 37, 37, 55, 55, 108, 112, 1, 1] 112 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: 393 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054585 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054585 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054585/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054585 Building REAL250005054586 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054586' /scratch/stefan/7922901/working/building/REAL250005054586 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054586 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054586/0 /scratch/stefan/7922901/working/building/REAL250005054586 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/731 `/scratch/stefan/7922901/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054586.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054586 none C#CCOCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 137, 99, 99, 50, 36, 50, 30, 36, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 99, 99, 99, 99, 36, 36, 36, 30, 30, 16, 16, 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: 790 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054586 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054586 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054586/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054586 Building REAL250005054587 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054587' /scratch/stefan/7922901/working/building/REAL250005054587 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054587 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054587/0 /scratch/stefan/7922901/working/building/REAL250005054587 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/732 `/scratch/stefan/7922901/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054587.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054587 none C#CCOC(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 114, 102, 86, 102, 64, 86, 38, 64, 25, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 157, 157, 157, 102, 102, 102, 102, 64, 64, 64, 38, 38, 25, 25, 6, 1] 157 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054587 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054587 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054587/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054587 Building REAL250005054588 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054588' /scratch/stefan/7922901/working/building/REAL250005054588 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054588 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054588/0 /scratch/stefan/7922901/working/building/REAL250005054588 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/733 `/scratch/stefan/7922901/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)C(N)=O) `REAL250005054588.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054588 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)C(N)=O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 4, 6, 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: [29, 25, 14, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 29, 39, 39, 43, 43, 43, 47, 47, 29, 29, 29, 25, 25, 14, 14, 7, 1, 43, 43, 43, 43, 43, 43, 47, 47] 47 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 194 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054588 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054588 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054588/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054588 Building REAL250005054589 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054589' /scratch/stefan/7922901/working/building/REAL250005054589 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054589 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054589/0 /scratch/stefan/7922901/working/building/REAL250005054589 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/734 `/scratch/stefan/7922901/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C2CC2)CC1) `REAL250005054589.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054589 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 33, 88, 121, 201, 201, 201, 201, 201, 201, 201, 201, 11, 17, 1, 1, 1, 1, 11, 11, 33, 33, 33, 88, 88, 121, 121, 201, 201, 1, 1, 1, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 774 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054589 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 10, 34, 61, 149, 149, 149, 155, 155, 155, 155, 155, 1, 4, 1, 1, 11, 11, 1, 1, 10, 10, 10, 34, 34, 61, 61, 149, 155, 11, 11, 11, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 13, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 553 number of broken/clashed sets: 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: REAL250005054589 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C2CC2)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 36, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 78, 146, 146, 155, 201, 201, 155, 155, 78, 78, 78, 36, 36, 20, 20, 5, 1, 201, 201, 201, 201, 201, 155, 155, 155, 155] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 706 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054589 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054589 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054589/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054589 Building REAL250005054590 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054590' /scratch/stefan/7922901/working/building/REAL250005054590 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054590 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054590/0 /scratch/stefan/7922901/working/building/REAL250005054590 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/735 `/scratch/stefan/7922901/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054590.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054590 none COC1CC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 146, 82, 146, 45, 82, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 82, 82, 82, 45, 45, 29, 29, 9, 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: 704 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: REAL250005054590 none COC1CC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 24, 24, 74, 108, 194, 196, 194, 201, 201, 201, 201, 201, 1, 5, 5, 5, 1, 1, 1, 1, 24, 24, 24, 74, 74, 108, 108, 196, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 20, 24, 25, 26, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 745 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054590 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054590 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054590/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054590 Building REAL250005054591 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054591' /scratch/stefan/7922901/working/building/REAL250005054591 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054591 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054591/0 /scratch/stefan/7922901/working/building/REAL250005054591 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/736 `/scratch/stefan/7922901/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1C[C@H]1C(N)=O) `REAL250005054591.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054591 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 12, 27, 39, 63, 63, 63, 73, 73, 73, 73, 73, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 27, 27, 39, 39, 63, 73, 1, 1, 7, 7] 80 rigid atoms, others: [32, 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, 34, 35]) total number of confs: 272 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: REAL250005054591 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1C[C@H]1C(N)=O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [48, 32, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 48, 65, 65, 73, 73, 73, 73, 73, 80, 80, 48, 48, 48, 32, 32, 19, 19, 7, 1, 73, 73, 80, 80] 80 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 308 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054591 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054591 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054591/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054591 Building REAL250005054592 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054592' /scratch/stefan/7922901/working/building/REAL250005054592 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054592 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054592/0 /scratch/stefan/7922901/working/building/REAL250005054592 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/737 `/scratch/stefan/7922901/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005054592.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054592 none CC[C@@H](C(=O)N(C)CCNC(=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', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 5, 7, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 8, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 3, 1, 9, 9, 9, 9, 9, 9] 9 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: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054592 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054592 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054592/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054592 Building REAL250005054593 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054593' /scratch/stefan/7922901/working/building/REAL250005054593 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054593 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054593/0 /scratch/stefan/7922901/working/building/REAL250005054593 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/738 `/scratch/stefan/7922901/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CF)CCC1) `REAL250005054593.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054593 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CF)CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 5, 17, 31, 110, 110, 110, 131, 131, 131, 131, 131, 1, 3, 1, 1, 8, 1, 1, 1, 5, 5, 5, 17, 17, 31, 31, 110, 131, 8, 8, 1, 1, 1, 1, 1, 1] 142 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 403 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: REAL250005054593 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CF)CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 15, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [88, 46, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 87, 131, 131, 131, 142, 131, 131, 131, 88, 88, 88, 46, 46, 27, 27, 8, 1, 142, 142, 131, 131, 131, 131, 131, 131] 142 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 544 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054593 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054593 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054593/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054593 Building REAL250005054594 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054594' /scratch/stefan/7922901/working/building/REAL250005054594 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054594 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054594/0 /scratch/stefan/7922901/working/building/REAL250005054594 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/739 `/scratch/stefan/7922901/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054594.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054594 none CC[C@@H]1C[C@H]1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 172, 172, 172, 172, 108, 172, 69, 108, 34, 69, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 172, 172, 69, 69, 69, 35, 35, 20, 20, 5, 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: 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: REAL250005054594 none CC[C@@H]1C[C@H]1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 28, 28, 67, 90, 163, 163, 163, 172, 172, 172, 172, 172, 3, 3, 3, 3, 3, 1, 1, 28, 28, 28, 67, 67, 90, 90, 163, 172] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 602 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054594 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054594 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054594/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054594 Building REAL250005054595 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054595' /scratch/stefan/7922901/working/building/REAL250005054595 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054595 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054595/0 /scratch/stefan/7922901/working/building/REAL250005054595 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/740 `/scratch/stefan/7922901/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054595.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054595 none CC(C)CCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 196, 184, 166, 152, 70, 58, 70, 32, 58, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 198, 201, 201, 201, 201, 196, 195, 184, 184, 153, 153, 58, 58, 58, 32, 32, 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: 1111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054595 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054595 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054595/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054595 Building REAL250005054596 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054596' /scratch/stefan/7922901/working/building/REAL250005054596 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054596 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054596/0 /scratch/stefan/7922901/working/building/REAL250005054596 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/741 `/scratch/stefan/7922901/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=NC=N1) `REAL250005054596.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054596 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=NC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 46, 97, 127, 201, 201, 201, 201, 201, 201, 201, 201, 8, 25, 1, 1, 1, 1, 1, 1, 46, 46, 46, 97, 97, 127, 127, 201, 201, 8, 8, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 786 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054596 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=NC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 53, 110, 110, 171, 201, 201, 201, 201, 53, 53, 53, 25, 25, 14, 14, 4, 1, 171, 171, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 714 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054596 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054596 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054596/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054596 Building REAL250005054597 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054597' /scratch/stefan/7922901/working/building/REAL250005054597 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054597 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054597/0 /scratch/stefan/7922901/working/building/REAL250005054597 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/742 `/scratch/stefan/7922901/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCNC(N)=O) `REAL250005054597.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054597 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCNC(N)=O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [39, 19, 10, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 53, 53, 55, 79, 105, 105, 105, 39, 39, 39, 19, 19, 10, 10, 4, 1, 55, 55, 79, 79, 105, 105, 105] 105 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054597 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054597 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054597/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054597 Building REAL250005054598 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054598' /scratch/stefan/7922901/working/building/REAL250005054598 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054598 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054598/0 /scratch/stefan/7922901/working/building/REAL250005054598 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/743 `/scratch/stefan/7922901/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NSC=C1) `REAL250005054598.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054598 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NSC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 9, 23, 63, 95, 181, 181, 181, 193, 193, 193, 193, 193, 1, 9, 1, 1, 1, 1, 1, 23, 23, 23, 63, 63, 95, 95, 181, 193, 1, 1] 193 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005054598 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NSC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [113, 56, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 113, 185, 185, 193, 193, 193, 193, 113, 113, 113, 56, 56, 36, 36, 11, 1, 193, 193] 193 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 629 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054598 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054598 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054598/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054598 Building REAL250005054599 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054599' /scratch/stefan/7922901/working/building/REAL250005054599 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054599 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054599/0 /scratch/stefan/7922901/working/building/REAL250005054599 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/744 `/scratch/stefan/7922901/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)C1CCC1) `REAL250005054599.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054599 none CC(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 7, 7, 14, 14, 29, 39, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 3, 3, 3, 3, 14, 14, 14, 29, 29, 39, 39, 73, 73, 1, 1, 1, 1, 1, 1, 1] 73 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: 266 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: REAL250005054599 none CC(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 71, 54, 71, 33, 54, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 73, 73, 73, 54, 54, 54, 33, 33, 19, 19, 4, 1, 73, 73, 73, 73, 73, 73, 73] 73 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: 273 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054599 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054599 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054599/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054599 Building REAL250005054600 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054600' /scratch/stefan/7922901/working/building/REAL250005054600 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054600 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054600/0 /scratch/stefan/7922901/working/building/REAL250005054600 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/745 `/scratch/stefan/7922901/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CO1) `REAL250005054600.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054600 none CC1CC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 80, 55, 80, 30, 55, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 105, 105, 105, 55, 55, 55, 30, 30, 20, 20, 6, 1, 105, 105] 105 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: 376 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: REAL250005054600 none CC1CC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 18, 18, 36, 55, 101, 101, 101, 105, 105, 105, 105, 105, 1, 1, 2, 2, 2, 1, 1, 1, 1, 18, 18, 18, 36, 36, 55, 55, 101, 105, 1, 1] 105 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 19, 20, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 376 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054600 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054600 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054600/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054600 Building REAL250005054601 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054601' /scratch/stefan/7922901/working/building/REAL250005054601 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054601 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054601/0 /scratch/stefan/7922901/working/building/REAL250005054601 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/746 `/scratch/stefan/7922901/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC12CC2) `REAL250005054601.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054601 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC12CC2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 53, 76, 141, 141, 141, 146, 146, 146, 146, 146, 1, 8, 1, 1, 1, 1, 1, 20, 20, 20, 53, 53, 76, 76, 141, 146, 1, 1, 1, 1, 1, 1, 1] 146 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 537 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: REAL250005054601 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC12CC2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [66, 36, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 65, 114, 115, 146, 146, 146, 146, 66, 66, 66, 36, 36, 23, 23, 7, 1, 146, 146, 146, 146, 146, 146, 146] 146 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 514 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054601 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054601 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054601/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054601 Building REAL250005054602 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054602' /scratch/stefan/7922901/working/building/REAL250005054602 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054602 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054602/0 /scratch/stefan/7922901/working/building/REAL250005054602 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/747 `/scratch/stefan/7922901/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CN=CN1) `REAL250005054602.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054602 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CN=CN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 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: [51, 22, 51, 99, 123, 201, 201, 201, 201, 201, 201, 201, 201, 4, 22, 1, 1, 1, 1, 1, 1, 51, 51, 51, 99, 99, 123, 123, 201, 201, 4, 4, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 753 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054602 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CN=CN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 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: [54, 23, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 54, 110, 110, 156, 201, 201, 201, 201, 54, 54, 54, 23, 23, 11, 11, 4, 1, 156, 156, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 689 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054602 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054602 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054602/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054602 Building REAL250005054603 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054603' /scratch/stefan/7922901/working/building/REAL250005054603 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054603 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054603/0 /scratch/stefan/7922901/working/building/REAL250005054603 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/748 `/scratch/stefan/7922901/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054603.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054603 none C=CCC(C)(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 37, 37, 37, 37, 27, 37, 15, 27, 9, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 37, 37, 37, 37, 37, 37, 27, 27, 27, 15, 15, 9, 9, 2, 1] 45 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: 197 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054603 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054603 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054603/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054603 Building REAL250005054604 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054604' /scratch/stefan/7922901/working/building/REAL250005054604 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054604 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054604/0 /scratch/stefan/7922901/working/building/REAL250005054604 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/749 `/scratch/stefan/7922901/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC12CCC2) `REAL250005054604.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054604 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC12CCC2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 7, 18, 53, 76, 130, 130, 130, 133, 133, 133, 133, 133, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 53, 53, 76, 76, 130, 133, 1, 1, 1, 1, 1, 1, 1, 1, 1] 133 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 508 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054604 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC12CCC2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [51, 27, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 50, 98, 99, 133, 133, 133, 133, 133, 51, 51, 51, 27, 27, 18, 18, 7, 1, 133, 133, 133, 133, 133, 133, 133, 133, 133] 133 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 470 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054604 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054604 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054604/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054604 Building REAL250005054605 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054605' /scratch/stefan/7922901/working/building/REAL250005054605 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054605 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054605/0 /scratch/stefan/7922901/working/building/REAL250005054605 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/750 `/scratch/stefan/7922901/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNC=C1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054605.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054605 none CC1=CNC=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 181, 181, 181, 128, 71, 128, 41, 71, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 181, 71, 71, 71, 41, 41, 30, 30, 8, 1] 181 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: 526 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: REAL250005054605 none CC1=CNC=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 9, 9, 27, 27, 68, 95, 175, 177, 177, 181, 181, 181, 181, 181, 2, 2, 2, 1, 1, 1, 27, 27, 27, 68, 68, 95, 95, 177, 181] 181 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 680 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054605 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054605 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054605/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054605 Building REAL250005054606 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054606' /scratch/stefan/7922901/working/building/REAL250005054606 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054606 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054606/0 /scratch/stefan/7922901/working/building/REAL250005054606 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/751 `/scratch/stefan/7922901/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN(C)C=C1) `REAL250005054606.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054606 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN(C)C=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 30, 72, 103, 187, 187, 187, 201, 201, 201, 201, 201, 1, 12, 1, 1, 1, 1, 1, 1, 30, 30, 30, 72, 72, 103, 103, 187, 201, 2, 2, 2, 1, 1] 201 rigid atoms, others: [33, 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]) total number of confs: 716 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: REAL250005054606 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN(C)C=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 99, 184, 184, 201, 201, 201, 201, 201, 101, 101, 101, 53, 53, 31, 31, 10, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 665 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054606 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054606 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054606/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054606 Building REAL250005054607 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054607' /scratch/stefan/7922901/working/building/REAL250005054607 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054607 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054607/0 /scratch/stefan/7922901/working/building/REAL250005054607 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/752 `/scratch/stefan/7922901/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(F)CCCC1) `REAL250005054607.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054607 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(F)CCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 5, 16, 46, 80, 166, 166, 166, 173, 173, 173, 173, 173, 1, 5, 1, 1, 1, 1, 1, 1, 16, 16, 16, 46, 46, 80, 80, 166, 173, 1, 1, 1, 1, 1, 1, 1, 1] 173 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 612 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: REAL250005054607 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(F)CCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [83, 41, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 83, 143, 143, 173, 173, 173, 173, 173, 83, 83, 83, 41, 41, 23, 23, 7, 1, 173, 173, 173, 173, 173, 173, 173, 173] 173 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 622 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054607 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054607 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054607/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054607 Building REAL250005054608 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054608' /scratch/stefan/7922901/working/building/REAL250005054608 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054608 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054608/0 /scratch/stefan/7922901/working/building/REAL250005054608 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/753 `/scratch/stefan/7922901/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CN1C) `REAL250005054608.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054608 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CN1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 23, 73, 98, 195, 195, 195, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 73, 73, 98, 98, 195, 201, 1, 1, 2, 2, 2] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 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, 32, 33, 34]) total number of confs: 729 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: REAL250005054608 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CN1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 83, 179, 179, 201, 201, 201, 201, 201, 83, 83, 83, 44, 44, 30, 30, 8, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 616 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054608 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054608 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054608/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054608 Building REAL250005054609 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054609' /scratch/stefan/7922901/working/building/REAL250005054609 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054609 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054609/0 /scratch/stefan/7922901/working/building/REAL250005054609 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/754 `/scratch/stefan/7922901/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054609.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054609 none CN(C)C(=O)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 21, 11, 11, 11, 9, 11, 5, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 19, 19, 11, 11, 11, 9, 9, 5, 5, 2, 1] 21 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: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054609 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054609 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054609/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054609 Building REAL250005054610 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054610' /scratch/stefan/7922901/working/building/REAL250005054610 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054610 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054610/0 /scratch/stefan/7922901/working/building/REAL250005054610 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/755 `/scratch/stefan/7922901/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1C1CC1) `REAL250005054610.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054610 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 54, 114, 148, 201, 201, 201, 201, 201, 201, 201, 201, 6, 27, 6, 6, 6, 1, 6, 1, 1, 1, 54, 54, 54, 114, 114, 148, 148, 201, 201, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 817 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054610 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 22, 59, 85, 160, 160, 160, 168, 168, 168, 168, 168, 1, 8, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 59, 59, 85, 85, 160, 168, 1, 1, 6, 6, 6, 6, 6] 201 rigid atoms, others: [32, 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, 34, 35, 36, 37, 38]) total number of confs: 622 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: REAL250005054610 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 17, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 65, 105, 105, 168, 168, 168, 168, 168, 201, 201, 65, 65, 65, 34, 34, 17, 17, 4, 1, 168, 168, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 738 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054610 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054610 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054610/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054610 Building REAL250005054611 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054611' /scratch/stefan/7922901/working/building/REAL250005054611 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054611 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054611/0 /scratch/stefan/7922901/working/building/REAL250005054611 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/756 `/scratch/stefan/7922901/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054611.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054611 none COCCC(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 28, 18, 28, 15, 18, 14, 15, 10, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 41, 28, 28, 28, 28, 15, 15, 15, 14, 14, 10, 10, 3, 1] 50 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: 241 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054611 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054611 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054611/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054611 Building REAL250005054612 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054612' /scratch/stefan/7922901/working/building/REAL250005054612 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054612 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054612/0 /scratch/stefan/7922901/working/building/REAL250005054612 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/757 `/scratch/stefan/7922901/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CC)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054612.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054612 none CCC(C)(CC)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [103, 89, 67, 89, 89, 103, 53, 67, 29, 53, 18, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 89, 89, 89, 103, 103, 103, 103, 103, 53, 53, 53, 29, 29, 18, 18, 6, 1] 111 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: 550 number of broken/clashed sets: 111 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054612 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054612 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054612/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054612 Building REAL250005054613 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054613' /scratch/stefan/7922901/working/building/REAL250005054613 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054613 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054613/0 /scratch/stefan/7922901/working/building/REAL250005054613 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/758 `/scratch/stefan/7922901/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054613.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054613 none COCC1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [103, 103, 77, 71, 52, 71, 26, 52, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 77, 77, 103, 103, 103, 103, 103, 52, 52, 52, 26, 26, 19, 19, 4, 1, 77, 77, 77, 77] 103 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: 427 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: REAL250005054613 none COCC1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [24, 10, 1, 1, 1, 3, 3, 7, 7, 22, 28, 70, 70, 70, 77, 77, 77, 77, 77, 1, 1, 24, 24, 24, 10, 10, 7, 7, 7, 22, 22, 28, 28, 70, 77, 1, 1, 1, 1] 103 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: 295 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054613 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054613 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054613/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054613 Building REAL250005054614 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054614' /scratch/stefan/7922901/working/building/REAL250005054614 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054614 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054614/0 /scratch/stefan/7922901/working/building/REAL250005054614 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/759 `/scratch/stefan/7922901/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054614.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054614 none COCC(C)(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 29, 29, 29, 29, 23, 29, 15, 23, 10, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 29, 29, 29, 29, 29, 29, 23, 23, 23, 15, 15, 10, 10, 2, 1] 38 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: 172 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054614 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054614 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054614/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054614 Building REAL250005054615 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054615' /scratch/stefan/7922901/working/building/REAL250005054615 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054615 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054615/0 /scratch/stefan/7922901/working/building/REAL250005054615 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/760 `/scratch/stefan/7922901/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCCO1) `REAL250005054615.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054615 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 14, 38, 55, 109, 109, 109, 117, 117, 117, 117, 117, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 38, 38, 55, 55, 109, 117, 1, 1, 1, 1, 1, 1] 117 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 408 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054615 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [77, 42, 31, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 77, 114, 114, 117, 117, 117, 117, 117, 77, 77, 77, 42, 42, 31, 31, 8, 1, 117, 117, 117, 117, 117, 117] 117 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054615 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054615 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054615/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054615 Building REAL250005054616 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054616' /scratch/stefan/7922901/working/building/REAL250005054616 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054616 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054616/0 /scratch/stefan/7922901/working/building/REAL250005054616 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/761 `/scratch/stefan/7922901/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC(F)F) `REAL250005054616.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054616 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC(F)F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 59, 101, 101, 143, 177, 201, 201, 59, 59, 59, 28, 28, 14, 14, 4, 1, 143, 143, 181, 181, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 915 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054616 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054616 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054616/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054616 Building REAL250005054617 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054617' /scratch/stefan/7922901/working/building/REAL250005054617 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054617 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054617/0 /scratch/stefan/7922901/working/building/REAL250005054617 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/762 `/scratch/stefan/7922901/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC(F)=CN1) `REAL250005054617.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054617 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC(F)=CN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 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: [31, 11, 31, 74, 109, 199, 199, 199, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 31, 31, 31, 74, 74, 109, 109, 199, 201, 1, 1, 1] 201 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 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]) 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: REAL250005054617 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC(F)=CN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 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: [82, 41, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 82, 160, 160, 201, 201, 201, 201, 201, 82, 82, 82, 41, 41, 26, 26, 6, 1, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 591 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054617 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054617 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054617/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054617 Building REAL250005054618 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054618' /scratch/stefan/7922901/working/building/REAL250005054618 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054618 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054618/0 /scratch/stefan/7922901/working/building/REAL250005054618 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/763 `/scratch/stefan/7922901/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1(C)CC1) `REAL250005054618.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054618 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1(C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 43, 100, 138, 200, 200, 200, 201, 201, 201, 201, 201, 6, 21, 1, 1, 1, 1, 1, 43, 43, 43, 100, 100, 138, 138, 200, 201, 6, 6, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 789 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054618 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1(C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 75, 132, 132, 167, 201, 201, 201, 75, 75, 75, 42, 42, 24, 24, 6, 1, 167, 167, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 759 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054618 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054618 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054618/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054618 Building REAL250005054619 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054619' /scratch/stefan/7922901/working/building/REAL250005054619 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054619 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054619/0 /scratch/stefan/7922901/working/building/REAL250005054619 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/764 `/scratch/stefan/7922901/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CCF)CC1) `REAL250005054619.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054619 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CCF)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 3, 8, 24, 36, 78, 78, 78, 82, 82, 82, 82, 82, 1, 3, 1, 1, 7, 18, 1, 1, 8, 8, 8, 24, 24, 36, 36, 78, 82, 7, 7, 18, 18, 1, 1, 1, 1] 110 rigid atoms, others: [34, 35, 36, 37, 13, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 351 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: REAL250005054619 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CCF)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [56, 28, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 56, 80, 80, 82, 110, 110, 82, 82, 56, 56, 56, 28, 28, 14, 14, 4, 1, 110, 110, 110, 110, 82, 82, 82, 82] 110 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 456 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054619 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054619 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054619/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054619 Building REAL250005054620 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054620' /scratch/stefan/7922901/working/building/REAL250005054620 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054620 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054620/0 /scratch/stefan/7922901/working/building/REAL250005054620 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/765 `/scratch/stefan/7922901/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@]12C[C@H]1COC2) `REAL250005054620.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054620 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@]12C[C@H]1COC2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 28, 46, 88, 88, 88, 91, 91, 91, 91, 91, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 28, 28, 46, 46, 88, 91, 1, 1, 1, 1, 1, 1] 91 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054620 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@]12C[C@H]1COC2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [52, 29, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 52, 91, 91, 91, 91, 91, 91, 91, 91, 52, 52, 52, 29, 29, 16, 16, 6, 1, 91, 91, 91, 91, 91, 91] 91 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054620 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054620 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054620/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054620 Building REAL250005054621 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054621' /scratch/stefan/7922901/working/building/REAL250005054621 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054621 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054621/0 /scratch/stefan/7922901/working/building/REAL250005054621 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/766 `/scratch/stefan/7922901/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CC1) `REAL250005054621.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054621 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 3, 7, 22, 35, 72, 72, 72, 74, 74, 74, 74, 74, 1, 3, 1, 1, 1, 1, 7, 7, 7, 22, 22, 35, 35, 72, 74, 2, 2, 2, 1, 1, 1, 1] 74 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL250005054621 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [52, 31, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 52, 73, 73, 74, 74, 74, 52, 52, 52, 31, 31, 20, 20, 6, 1, 74, 74, 74, 74, 74, 74, 74] 74 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054621 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054621 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054621/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054621 Building REAL250005054622 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054622' /scratch/stefan/7922901/working/building/REAL250005054622 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054622 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054622/0 /scratch/stefan/7922901/working/building/REAL250005054622 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/767 `/scratch/stefan/7922901/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNC=C1) `REAL250005054622.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054622 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [31, 11, 31, 69, 99, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 31, 31, 31, 69, 69, 99, 99, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 727 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: REAL250005054622 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [63, 29, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 63, 123, 123, 201, 201, 201, 201, 63, 63, 63, 29, 29, 16, 16, 4, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 574 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054622 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054622 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054622/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054622 Building REAL250005054623 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054623' /scratch/stefan/7922901/working/building/REAL250005054623 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054623 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054623/0 /scratch/stefan/7922901/working/building/REAL250005054623 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/768 `/scratch/stefan/7922901/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005054623.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054623 none CC(CC(=O)N(C)CCNC(=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', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 14, 27, 27, 34, 34, 76, 96, 158, 158, 158, 160, 160, 160, 160, 160, 1, 1, 1, 5, 5, 5, 4, 14, 14, 34, 34, 34, 76, 76, 96, 96, 158, 160, 1, 1, 1, 1, 1] 160 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: 616 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054623 none CC(CC(=O)N(C)CCNC(=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', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [157, 141, 76, 66, 76, 42, 66, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 157, 160, 160, 157, 157, 157, 157, 142, 142, 66, 66, 66, 42, 42, 25, 25, 7, 1, 160, 160, 160, 160, 160] 160 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: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054623 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054623 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054623/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054623 Building REAL250005054624 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054624' /scratch/stefan/7922901/working/building/REAL250005054624 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054624 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054624/0 /scratch/stefan/7922901/working/building/REAL250005054624 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/769 `/scratch/stefan/7922901/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CSN=N1) `REAL250005054624.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054624 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CSN=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 14, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 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: [31, 12, 31, 74, 108, 188, 188, 188, 201, 201, 201, 201, 201, 1, 12, 1, 1, 1, 1, 1, 31, 31, 31, 74, 74, 108, 108, 188, 201, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005054624 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CSN=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 14, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 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: [104, 53, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 104, 179, 179, 201, 201, 201, 201, 104, 104, 104, 53, 53, 32, 32, 9, 1, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29]) total number of confs: 652 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054624 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054624 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054624/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054624 Building REAL250005054625 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054625' /scratch/stefan/7922901/working/building/REAL250005054625 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054625 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054625/0 /scratch/stefan/7922901/working/building/REAL250005054625 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/770 `/scratch/stefan/7922901/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CCCC1) `REAL250005054625.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054625 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 3, 4, 10, 17, 38, 38, 38, 40, 40, 40, 40, 40, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 17, 17, 38, 40, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 40 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 145 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: REAL250005054625 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 23, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 38, 40, 40, 40, 40, 40, 40, 40, 38, 38, 38, 23, 23, 17, 17, 6, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 40 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054625 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054625 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054625/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054625 Building REAL250005054626 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054626' /scratch/stefan/7922901/working/building/REAL250005054626 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054626 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054626/0 /scratch/stefan/7922901/working/building/REAL250005054626 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/771 `/scratch/stefan/7922901/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CO1) `REAL250005054626.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054626 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 12, 28, 72, 105, 197, 197, 197, 201, 201, 201, 201, 201, 1, 12, 1, 1, 1, 1, 1, 28, 28, 28, 72, 72, 105, 105, 197, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 735 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054626 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 50, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 92, 178, 178, 201, 201, 201, 201, 92, 92, 92, 50, 50, 32, 32, 9, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 632 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054626 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054626 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054626/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054626 Building REAL250005054627 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054627' /scratch/stefan/7922901/working/building/REAL250005054627 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054627 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054627/0 /scratch/stefan/7922901/working/building/REAL250005054627 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/772 `/scratch/stefan/7922901/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054627.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054627 none CNC(=O)NCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 43, 43, 43, 25, 21, 17, 21, 15, 17, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 43, 25, 25, 17, 17, 17, 15, 15, 13, 13, 4, 1] 47 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: 167 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054627 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054627 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054627/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054627 Building REAL250005054628 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054628' /scratch/stefan/7922901/working/building/REAL250005054628 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054628 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054628/0 /scratch/stefan/7922901/working/building/REAL250005054628 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/773 `/scratch/stefan/7922901/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054628.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054628 none C=CCCOCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 137, 80, 54, 16, 14, 16, 14, 14, 10, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 137, 137, 54, 54, 14, 14, 14, 14, 14, 10, 10, 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: 858 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054628 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054628 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054628/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054628 Building REAL250005054629 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054629' /scratch/stefan/7922901/working/building/REAL250005054629 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054629 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054629/0 /scratch/stefan/7922901/working/building/REAL250005054629 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/774 `/scratch/stefan/7922901/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054629.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054629 none C=CCOC(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 125, 105, 82, 105, 59, 82, 38, 59, 19, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 105, 105, 105, 105, 59, 59, 59, 38, 38, 19, 19, 5, 1] 192 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: 832 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054629 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054629 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054629/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054629 Building REAL250005054630 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054630' /scratch/stefan/7922901/working/building/REAL250005054630 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054630 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054630/0 /scratch/stefan/7922901/working/building/REAL250005054630 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/775 `/scratch/stefan/7922901/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCC(N)=O) `REAL250005054630.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054630 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCC(N)=O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 19, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 61, 61, 65, 87, 149, 201, 201, 41, 41, 41, 19, 19, 12, 12, 4, 1, 65, 65, 87, 87, 149, 149, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 884 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054630 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054630 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054630/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054630 Building REAL250005054631 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054631' /scratch/stefan/7922901/working/building/REAL250005054631 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054631 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054631/0 /scratch/stefan/7922901/working/building/REAL250005054631 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/776 `/scratch/stefan/7922901/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC=C1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054631.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054631 none CC1=NNC=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 175, 135, 70, 135, 41, 70, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 70, 70, 70, 41, 41, 25, 25, 9, 1] 175 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: 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: REAL250005054631 none CC1=NNC=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 9, 9, 23, 23, 63, 97, 169, 171, 169, 175, 175, 175, 175, 175, 2, 2, 2, 1, 1, 23, 23, 23, 63, 63, 97, 97, 171, 175] 175 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: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054631 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054631 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054631/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054631 Building REAL250005054632 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054632' /scratch/stefan/7922901/working/building/REAL250005054632 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054632 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054632/0 /scratch/stefan/7922901/working/building/REAL250005054632 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/777 `/scratch/stefan/7922901/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNN=C1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054632.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054632 none CC1=NNN=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 82, 141, 39, 82, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 82, 82, 82, 39, 39, 25, 25, 5, 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: 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: REAL250005054632 none CC1=NNN=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 25, 25, 81, 116, 197, 197, 197, 201, 201, 201, 201, 201, 2, 2, 2, 1, 25, 25, 25, 81, 81, 116, 116, 197, 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: 754 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054632 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054632/1 /scratch/stefan/7922901/working/building/REAL250005054632 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/778 `/scratch/stefan/7922901/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)NN=N1) `REAL250005054632.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054632 none CC1=C(C(=O)N(C)CCNC(=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', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 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, 158, 82, 158, 45, 82, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 82, 82, 82, 45, 45, 28, 28, 9, 1, 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]) total number of confs: 609 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: REAL250005054632 none CC1=C(C(=O)N(C)CCNC(=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', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 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, 9, 9, 29, 29, 77, 101, 195, 195, 195, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 29, 29, 29, 77, 77, 101, 101, 195, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 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: 711 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054632 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054632 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054632/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054632/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054632 Building REAL250005054633 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054633' /scratch/stefan/7922901/working/building/REAL250005054633 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054633 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054633/0 /scratch/stefan/7922901/working/building/REAL250005054633 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/779 `/scratch/stefan/7922901/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(OC)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054633.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054633 none CCCC(OC)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 136, 91, 75, 91, 106, 60, 75, 38, 60, 24, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 136, 136, 91, 106, 106, 106, 60, 60, 60, 38, 38, 24, 24, 7, 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: 677 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054633 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054633 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054633/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054633 Building REAL250005054634 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054634' /scratch/stefan/7922901/working/building/REAL250005054634 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054634 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054634/0 /scratch/stefan/7922901/working/building/REAL250005054634 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/780 `/scratch/stefan/7922901/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C(C)(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054634.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054634 none C=C(C)C(C)(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 66, 66, 50, 66, 27, 50, 18, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 50, 50, 50, 27, 27, 18, 18, 7, 1] 66 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: 254 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054634 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054634 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054634/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054634 Building REAL250005054635 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054635' /scratch/stefan/7922901/working/building/REAL250005054635 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054635 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054635/0 /scratch/stefan/7922901/working/building/REAL250005054635 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/781 `/scratch/stefan/7922901/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(N)=O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054635.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054635 none CC(CC(N)=O)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [45, 34, 45, 56, 68, 68, 27, 34, 19, 27, 11, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 56, 56, 68, 68, 27, 27, 27, 19, 19, 11, 11, 4, 1] 68 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: 293 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054635 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054635 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054635/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054635 Building REAL250005054636 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054636' /scratch/stefan/7922901/working/building/REAL250005054636 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054636 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054636/0 /scratch/stefan/7922901/working/building/REAL250005054636 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/782 `/scratch/stefan/7922901/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCNC1=O) `REAL250005054636.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054636 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCNC1=O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 60, 95, 181, 181, 181, 199, 199, 199, 199, 199, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 60, 60, 95, 95, 181, 199, 1, 1, 1, 1, 1, 1] 199 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 725 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054636 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCNC1=O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [95, 51, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 95, 176, 176, 199, 199, 199, 199, 199, 95, 95, 95, 51, 51, 30, 30, 8, 1, 199, 199, 199, 199, 199, 199] 199 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 693 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054636 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054636 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054636/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054636 Building REAL250005054637 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054637' /scratch/stefan/7922901/working/building/REAL250005054637 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054637 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054637/0 /scratch/stefan/7922901/working/building/REAL250005054637 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/783 `/scratch/stefan/7922901/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054637.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054637 none C=CC(C)(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 97, 74, 97, 39, 74, 28, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97, 97, 97, 97, 74, 74, 74, 39, 39, 28, 28, 9, 1] 97 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: 354 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054637 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054637 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054637/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054637 Building REAL250005054638 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054638' /scratch/stefan/7922901/working/building/REAL250005054638 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054638 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054638/0 /scratch/stefan/7922901/working/building/REAL250005054638 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/784 `/scratch/stefan/7922901/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCC[N@@H+]1C) `REAL250005054638.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054638 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCC[N@@H+]1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2] 7 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 23 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: REAL250005054638 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCC[N@@H+]1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] 7 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 23 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054638 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054638/1 /scratch/stefan/7922901/working/building/REAL250005054638 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/785 `/scratch/stefan/7922901/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCC[N@H+]1C) `REAL250005054638.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054638 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCC[N@H+]1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 7, 7, 9, 9, 9, 12, 12, 12, 12, 12, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 9, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2] 12 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 46 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: REAL250005054638 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCC[N@H+]1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 8, 8, 5, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054638 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054638 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054638/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054638/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054638 Building REAL250005054639 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054639' /scratch/stefan/7922901/working/building/REAL250005054639 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054639 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054639/0 /scratch/stefan/7922901/working/building/REAL250005054639 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/786 `/scratch/stefan/7922901/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054639.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054639 none C[C@@H]1C[C@H]1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 87, 121, 55, 87, 32, 55, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 55, 55, 55, 32, 32, 20, 20, 6, 1] 121 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: 456 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: REAL250005054639 none C[C@@H]1C[C@H]1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 18, 18, 41, 55, 117, 117, 117, 121, 121, 121, 121, 121, 2, 2, 2, 1, 1, 18, 18, 18, 41, 41, 55, 55, 117, 121] 121 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: 426 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054639 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054639 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054639/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054639 Building REAL250005054640 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054640' /scratch/stefan/7922901/working/building/REAL250005054640 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054640 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054640/0 /scratch/stefan/7922901/working/building/REAL250005054640 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/787 `/scratch/stefan/7922901/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CCC1) `REAL250005054640.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054640 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 4, 7, 23, 39, 87, 87, 87, 92, 92, 92, 92, 92, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 39, 39, 87, 92, 2, 2, 2, 1, 1, 1, 1, 1, 1] 92 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 332 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: REAL250005054640 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 31, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 53, 92, 92, 92, 92, 92, 92, 53, 53, 53, 31, 31, 22, 22, 8, 1, 92, 92, 92, 92, 92, 92, 92, 92, 92] 92 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 326 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054640 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054640 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054640/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054640 Building REAL250005054641 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054641' /scratch/stefan/7922901/working/building/REAL250005054641 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054641 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054641/0 /scratch/stefan/7922901/working/building/REAL250005054641 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/788 `/scratch/stefan/7922901/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054641.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054641 none CCC(F)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [98, 95, 67, 96, 50, 67, 30, 50, 22, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 96, 50, 50, 50, 30, 30, 22, 22, 7, 1] 99 rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054641 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054641 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054641/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054641 Building REAL250005054642 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054642' /scratch/stefan/7922901/working/building/REAL250005054642 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054642 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054642/0 /scratch/stefan/7922901/working/building/REAL250005054642 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/789 `/scratch/stefan/7922901/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCF) `REAL250005054642.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054642 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCF NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 75, 137, 137, 159, 197, 201, 75, 75, 75, 36, 36, 20, 20, 4, 1, 159, 159, 197, 197, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 841 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054642 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054642 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054642/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054642 Building REAL250005054643 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054643' /scratch/stefan/7922901/working/building/REAL250005054643 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054643 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054643/0 /scratch/stefan/7922901/working/building/REAL250005054643 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/790 `/scratch/stefan/7922901/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC=C1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054643.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054643 none CC1=COC=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 190, 190, 142, 77, 142, 45, 77, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 190, 190, 190, 190, 190, 77, 77, 77, 45, 45, 30, 30, 9, 1] 190 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: 562 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: REAL250005054643 none CC1=COC=C1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 73, 100, 184, 186, 186, 190, 190, 190, 190, 190, 2, 2, 2, 1, 1, 27, 27, 27, 73, 73, 100, 100, 186, 190] 190 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: 708 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054643 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054643 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054643/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054643 Building REAL250005054644 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054644' /scratch/stefan/7922901/working/building/REAL250005054644 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054644 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054644/0 /scratch/stefan/7922901/working/building/REAL250005054644 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/791 `/scratch/stefan/7922901/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054644.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054644 none C[C@H]1C[C@@H]1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 87, 121, 56, 87, 32, 56, 20, 5, 6, 1, 5, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 56, 56, 56, 32, 32, 19, 19, 6, 1] 121 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: 455 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: REAL250005054644 none C[C@H]1C[C@@H]1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 18, 18, 41, 56, 117, 117, 117, 121, 121, 121, 121, 121, 2, 2, 2, 1, 1, 18, 18, 18, 41, 41, 56, 56, 117, 121] 121 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: 428 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054644 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054644 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054644/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054644 Building REAL250005054645 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054645' /scratch/stefan/7922901/working/building/REAL250005054645 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054645 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054645/0 /scratch/stefan/7922901/working/building/REAL250005054645 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/792 `/scratch/stefan/7922901/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)C=CCC1) `REAL250005054645.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054645 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)C=CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 4, 9, 16, 37, 37, 37, 39, 39, 39, 39, 39, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 16, 16, 37, 39, 2, 2, 2, 1, 1, 1, 1, 1, 1] 39 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 139 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054645 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)C=CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [36, 24, 16, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 36, 39, 39, 39, 39, 39, 39, 39, 36, 36, 36, 24, 24, 16, 16, 6, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39] 39 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 154 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054645 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054645 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054645/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054645 Building REAL250005054646 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054646' /scratch/stefan/7922901/working/building/REAL250005054646 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054646 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054646/0 /scratch/stefan/7922901/working/building/REAL250005054646 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/793 `/scratch/stefan/7922901/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN(C)N=N1) `REAL250005054646.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054646 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN(C)N=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 37, 80, 110, 201, 201, 201, 201, 201, 201, 201, 201, 1, 12, 1, 1, 1, 1, 1, 1, 37, 37, 37, 80, 80, 110, 110, 201, 201, 2, 2, 2] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20] set([0, 1, 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: 745 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054646 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN(C)N=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 68, 133, 133, 201, 201, 201, 201, 201, 68, 68, 68, 33, 33, 18, 18, 4, 1, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054646 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054646 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054646/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054646 Building REAL250005054647 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054647' /scratch/stefan/7922901/working/building/REAL250005054647 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054647 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054647/0 /scratch/stefan/7922901/working/building/REAL250005054647 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/794 `/scratch/stefan/7922901/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)NC=N1) `REAL250005054647.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054647 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 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 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 144, 83, 144, 44, 83, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 180, 180, 83, 83, 83, 44, 44, 32, 32, 11, 1, 180, 180] 180 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: 563 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054647 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 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 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, 9, 9, 29, 29, 66, 88, 166, 168, 166, 180, 180, 180, 180, 180, 1, 1, 1, 2, 2, 2, 29, 29, 29, 66, 66, 88, 88, 168, 180, 1, 1] 180 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: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054647 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054647 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054647/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054647 Building REAL250005054648 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054648' /scratch/stefan/7922901/working/building/REAL250005054648 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054648 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054648/0 /scratch/stefan/7922901/working/building/REAL250005054648 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/795 `/scratch/stefan/7922901/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(F)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054648.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054648 none CC(C)C(F)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 134, 175, 91, 135, 64, 91, 38, 64, 23, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 175, 175, 175, 174, 175, 175, 175, 135, 64, 64, 64, 38, 38, 23, 23, 7, 1] 175 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: 779 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054648 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054648 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054648/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054648 Building REAL250005054649 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054649' /scratch/stefan/7922901/working/building/REAL250005054649 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054649 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054649/0 /scratch/stefan/7922901/working/building/REAL250005054649 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/796 `/scratch/stefan/7922901/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)C(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054649.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054649 none C=CC(C)C(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 87, 92, 69, 87, 59, 69, 31, 59, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 92, 92, 87, 87, 87, 87, 59, 59, 59, 31, 31, 18, 18, 4, 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: 366 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054649 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054649 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054649/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054649 Building REAL250005054650 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054650' /scratch/stefan/7922901/working/building/REAL250005054650 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054650 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054650/0 /scratch/stefan/7922901/working/building/REAL250005054650 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/797 `/scratch/stefan/7922901/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005054650.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054650 none CCC1(C(=O)N(C)CCNC(=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', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 38, 47, 27, 38, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 38, 38, 38, 27, 27, 18, 18, 7, 1, 47, 47, 47, 47, 47, 47] 47 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: 171 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: REAL250005054650 none CCC1(C(=O)N(C)CCNC(=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', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 3, 3, 5, 5, 13, 20, 44, 44, 44, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 13, 13, 20, 20, 44, 47, 1, 1, 1, 1, 1, 1] 47 rigid atoms, others: [1, 2, 3, 36, 37, 35, 39, 40, 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: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054650 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054650 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054650/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054650 Building REAL250005054651 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054651' /scratch/stefan/7922901/working/building/REAL250005054651 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054651 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054651/0 /scratch/stefan/7922901/working/building/REAL250005054651 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/798 `/scratch/stefan/7922901/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054651.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054651 none CC#CCCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 95, 35, 27, 35, 23, 27, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 195, 126, 126, 96, 96, 27, 27, 27, 23, 23, 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: 975 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054651 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054651 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054651/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054651 Building REAL250005054652 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054652' /scratch/stefan/7922901/working/building/REAL250005054652 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054652 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054652/0 /scratch/stefan/7922901/working/building/REAL250005054652 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/799 `/scratch/stefan/7922901/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1[C@@H]2COC[C@@H]21) `REAL250005054652.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054652 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1[C@@H]2COC[C@@H]21 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 23, 69, 101, 195, 195, 195, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 69, 69, 101, 101, 195, 201, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 717 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: REAL250005054652 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1[C@@H]2COC[C@@H]21 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 42, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 77, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77, 77, 42, 42, 25, 25, 6, 1, 201, 201, 201, 201] 201 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 702 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054652 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054652 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054652/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054652 Building REAL250005054653 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054653' /scratch/stefan/7922901/working/building/REAL250005054653 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054653 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054653/0 /scratch/stefan/7922901/working/building/REAL250005054653 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/800 `/scratch/stefan/7922901/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCC1CC1) `REAL250005054653.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054653 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 47, 113, 144, 201, 201, 201, 201, 201, 201, 201, 201, 13, 37, 7, 3, 1, 1, 1, 1, 47, 47, 47, 113, 113, 145, 145, 201, 201, 13, 13, 7, 7, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 854 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054653 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 37, 51, 51, 53, 69, 113, 201, 201, 37, 37, 37, 21, 21, 10, 10, 4, 1, 53, 53, 69, 69, 113, 113, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 848 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054653 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054653 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054653/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054653 Building REAL250005054654 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054654' /scratch/stefan/7922901/working/building/REAL250005054654 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054654 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054654/0 /scratch/stefan/7922901/working/building/REAL250005054654 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/801 `/scratch/stefan/7922901/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC1(C)C) `REAL250005054654.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054654 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC1(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 4, 11, 30, 49, 89, 89, 89, 92, 92, 92, 92, 92, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 30, 30, 49, 49, 89, 92, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 92 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 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, 35, 36, 37, 38, 39, 40]) total number of confs: 362 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054654 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC1(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 30, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 53, 92, 92, 92, 92, 92, 92, 92, 53, 53, 53, 30, 30, 17, 17, 6, 1, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92] 92 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 320 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054654 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054654 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054654/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054654 Building REAL250005054655 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054655' /scratch/stefan/7922901/working/building/REAL250005054655 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054655 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054655/0 /scratch/stefan/7922901/working/building/REAL250005054655 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/802 `/scratch/stefan/7922901/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005054655.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054655 none CC1=COC(C(=O)N(C)CCNC(=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', '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, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 131, 83, 131, 47, 83, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 83, 83, 83, 47, 47, 28, 28, 7, 1, 141] 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, 34]) total number of confs: 473 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054655 none CC1=COC(C(=O)N(C)CCNC(=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', '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, 12, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 22, 22, 61, 83, 137, 137, 137, 141, 141, 141, 141, 141, 1, 2, 2, 2, 1, 22, 22, 22, 61, 61, 83, 83, 137, 141, 1] 141 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: 531 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054655 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054655 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054655/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054655 Building REAL250005054656 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054656' /scratch/stefan/7922901/working/building/REAL250005054656 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054656 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054656/0 /scratch/stefan/7922901/working/building/REAL250005054656 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/803 `/scratch/stefan/7922901/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(CC)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054656.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054656 none C=CC(CC)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [181, 171, 110, 170, 185, 55, 49, 55, 32, 49, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 181, 181, 181, 171, 185, 185, 185, 185, 185, 110, 110, 49, 49, 49, 32, 32, 20, 20, 4, 1] 185 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: 916 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054656 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054656 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054656/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054656 Building REAL250005054657 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054657' /scratch/stefan/7922901/working/building/REAL250005054657 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054657 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054657/0 /scratch/stefan/7922901/working/building/REAL250005054657 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/804 `/scratch/stefan/7922901/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)C1CC1) `REAL250005054657.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054657 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 10, 12, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 1, 6, 6, 1, 1, 1, 8, 8, 8, 10, 10, 12, 12, 15, 15, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1] 15 rigid atoms, others: [36, 37, 38, 39, 40, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 61 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: REAL250005054657 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 13, 13, 13, 13, 13, 15, 15, 9, 9, 9, 9, 9, 7, 7, 2, 1, 13, 13, 13, 13, 13, 13, 15, 15, 15, 15, 15] 15 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 55 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054657 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054657 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054657/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054657 Building REAL250005054658 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054658' /scratch/stefan/7922901/working/building/REAL250005054658 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054658 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054658/0 /scratch/stefan/7922901/working/building/REAL250005054658 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/805 `/scratch/stefan/7922901/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1C[C@H]2C[C@H]2C1) `REAL250005054658.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054658 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1C[C@H]2C[C@H]2C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 71, 107, 194, 194, 194, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 71, 71, 107, 107, 194, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 745 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: REAL250005054658 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1C[C@H]2C[C@H]2C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 46, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 95, 165, 167, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 97, 46, 46, 25, 25, 7, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 698 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054658 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054658 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054658/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054658 Building REAL250005054659 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054659' /scratch/stefan/7922901/working/building/REAL250005054659 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054659 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054659/0 /scratch/stefan/7922901/working/building/REAL250005054659 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/806 `/scratch/stefan/7922901/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CON=C1) `REAL250005054659.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054659 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CON=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 20, 64, 116, 135, 201, 201, 201, 201, 201, 201, 201, 201, 4, 20, 1, 1, 1, 1, 1, 1, 65, 65, 65, 116, 116, 135, 135, 201, 201, 4, 4, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 753 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054659 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CON=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 23, 12, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 45, 67, 67, 109, 201, 201, 201, 201, 45, 45, 45, 23, 23, 12, 12, 3, 1, 109, 109, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 624 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054659 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054659 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054659/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054659 Building REAL250005054660 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054660' /scratch/stefan/7922901/working/building/REAL250005054660 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054660 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054660/0 /scratch/stefan/7922901/working/building/REAL250005054660 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/807 `/scratch/stefan/7922901/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)C(C)(C)C) `REAL250005054660.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054660 none CC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 45, 56, 29, 45, 20, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 56, 56, 45, 45, 45, 29, 29, 20, 20, 8, 1, 56, 56, 56, 56, 56, 56, 56, 56, 56] 56 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: 212 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054660 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054660 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054660/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054660 Building REAL250005054661 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054661' /scratch/stefan/7922901/working/building/REAL250005054661 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054661 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054661/0 /scratch/stefan/7922901/working/building/REAL250005054661 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/808 `/scratch/stefan/7922901/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NNN=C1) `REAL250005054661.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054661 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NNN=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [27, 12, 27, 67, 101, 189, 189, 189, 201, 201, 201, 201, 201, 1, 12, 1, 1, 1, 1, 1, 27, 27, 27, 67, 67, 101, 101, 189, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005054661 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NNN=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [111, 56, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 111, 189, 189, 201, 201, 201, 201, 111, 111, 111, 56, 56, 34, 34, 9, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 675 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054661 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054661 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054661/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054661 Building REAL250005054662 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054662' /scratch/stefan/7922901/working/building/REAL250005054662 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054662 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054662/0 /scratch/stefan/7922901/working/building/REAL250005054662 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/809 `/scratch/stefan/7922901/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CC(N)=O) `REAL250005054662.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054662 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CC(N)=O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 6, 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: [23, 19, 16, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 25, 25, 30, 30, 30, 30, 23, 23, 23, 19, 19, 16, 16, 10, 1, 30, 30, 30, 30] 30 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054662 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054662 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054662/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054662 Building REAL250005054663 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054663' /scratch/stefan/7922901/working/building/REAL250005054663 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054663 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054663/0 /scratch/stefan/7922901/working/building/REAL250005054663 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/810 `/scratch/stefan/7922901/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC(N)=NN1) `REAL250005054663.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054663 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC(N)=NN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 7, 4, 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: [22, 8, 22, 59, 93, 187, 187, 187, 197, 197, 197, 197, 197, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 59, 59, 93, 93, 187, 197, 1, 1, 1] 197 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 695 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: REAL250005054663 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC(N)=NN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 7, 4, 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: [111, 56, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 111, 188, 188, 197, 197, 197, 197, 197, 111, 111, 111, 56, 56, 30, 30, 9, 1, 197, 197, 196] 197 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 654 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054663 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054663 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054663/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054663 Building REAL250005054664 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054664' /scratch/stefan/7922901/working/building/REAL250005054664 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054664 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054664/0 /scratch/stefan/7922901/working/building/REAL250005054664 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/811 `/scratch/stefan/7922901/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054664.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054664 none COC(=O)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 34, 51, 24, 24, 24, 13, 24, 9, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 51, 51, 51, 34, 34, 24, 24, 24, 13, 13, 9, 9, 3, 1] 51 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: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054664 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054664 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054664/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054664 Building REAL250005054665 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054665' /scratch/stefan/7922901/working/building/REAL250005054665 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054665 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054665/0 /scratch/stefan/7922901/working/building/REAL250005054665 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/812 `/scratch/stefan/7922901/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCSCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054665.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054665 none C#CCSCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 157, 71, 47, 39, 47, 27, 39, 16, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 73, 73, 39, 39, 39, 27, 27, 16, 16, 6, 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: 691 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054665 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054665 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054665/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054665 Building REAL250005054666 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054666' /scratch/stefan/7922901/working/building/REAL250005054666 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054666 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054666/0 /scratch/stefan/7922901/working/building/REAL250005054666 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/813 `/scratch/stefan/7922901/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054666.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054666 none CSC=CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 177, 177, 94, 65, 94, 41, 65, 26, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 193, 193, 193, 176, 177, 65, 65, 65, 41, 41, 26, 26, 9, 1] 193 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: 631 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054666 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054666 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054666/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054666 Building REAL250005054667 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054667' /scratch/stefan/7922901/working/building/REAL250005054667 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054667 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054667/0 /scratch/stefan/7922901/working/building/REAL250005054667 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/814 `/scratch/stefan/7922901/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CO)CCC1) `REAL250005054667.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054667 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CO)CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 20, 31, 52, 52, 52, 56, 56, 56, 56, 56, 1, 4, 1, 1, 9, 1, 1, 1, 7, 7, 7, 20, 20, 31, 31, 52, 56, 9, 9, 27, 1, 1, 1, 1, 1, 1] 189 rigid atoms, others: [33, 34, 35, 36, 37, 38, 13, 15, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 270 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: REAL250005054667 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CO)CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [36, 22, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 36, 56, 56, 56, 63, 56, 56, 56, 36, 36, 36, 22, 22, 15, 15, 5, 1, 63, 63, 189, 56, 56, 56, 56, 56, 56] 189 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 434 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054667 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054667 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054667/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054667 Building REAL250005054668 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054668' /scratch/stefan/7922901/working/building/REAL250005054668 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054668 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054668/0 /scratch/stefan/7922901/working/building/REAL250005054668 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/815 `/scratch/stefan/7922901/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC(N)=O) `REAL250005054668.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054668 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC(N)=O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 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: [71, 33, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 71, 104, 104, 104, 158, 201, 201, 71, 71, 71, 33, 33, 18, 18, 4, 1, 104, 104, 158, 158, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 816 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054668 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054668 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054668/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054668 Building REAL250005054669 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054669' /scratch/stefan/7922901/working/building/REAL250005054669 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054669 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054669/0 /scratch/stefan/7922901/working/building/REAL250005054669 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/816 `/scratch/stefan/7922901/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054669.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054669 none C=CCC1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [103, 103, 89, 80, 50, 80, 31, 50, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 89, 89, 103, 103, 103, 103, 103, 50, 50, 50, 31, 31, 19, 19, 4, 1, 89, 89, 89, 89] 103 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: 405 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: REAL250005054669 none C=CCC1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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: [24, 9, 1, 1, 1, 3, 3, 8, 8, 23, 35, 81, 81, 81, 89, 89, 89, 89, 89, 1, 1, 24, 24, 24, 9, 9, 8, 8, 8, 23, 23, 35, 35, 81, 89, 1, 1, 1, 1] 103 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: 362 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054669 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054669 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054669/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054669 Building REAL250005054670 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054670' /scratch/stefan/7922901/working/building/REAL250005054670 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054670 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054670/0 /scratch/stefan/7922901/working/building/REAL250005054670 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/817 `/scratch/stefan/7922901/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)COC(F)F) `REAL250005054670.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054670 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)COC(F)F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [41, 22, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 70, 70, 102, 181, 201, 201, 41, 41, 41, 22, 22, 12, 12, 4, 1, 102, 102, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 642 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054670 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054670 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054670/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054670 Building REAL250005054671 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054671' /scratch/stefan/7922901/working/building/REAL250005054671 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054671 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054671/0 /scratch/stefan/7922901/working/building/REAL250005054671 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/818 `/scratch/stefan/7922901/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCCS1) `REAL250005054671.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054671 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCCS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 25, 75, 110, 197, 198, 197, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 25, 25, 25, 75, 75, 110, 110, 198, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005054671 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCCS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 79, 145, 146, 201, 201, 201, 201, 80, 80, 80, 43, 43, 28, 28, 9, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054671 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054671 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054671/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054671 Building REAL250005054672 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054672' /scratch/stefan/7922901/working/building/REAL250005054672 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054672 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054672/0 /scratch/stefan/7922901/working/building/REAL250005054672 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/819 `/scratch/stefan/7922901/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054672.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054672 none CC1=NOC(C(=O)N(C)CCNC(=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', '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, 8, 12, 5, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 77, 58, 77, 34, 58, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 58, 58, 58, 34, 34, 23, 23, 6, 1, 90, 90] 90 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: 321 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: REAL250005054672 none CC1=NOC(C(=O)N(C)CCNC(=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', '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, 8, 12, 5, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 17, 17, 35, 51, 87, 87, 87, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 17, 17, 17, 35, 35, 51, 51, 87, 90, 1, 1] 90 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 35, 20, 21, 22, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 324 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054672 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054672 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054672/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054672 Building REAL250005054673 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054673' /scratch/stefan/7922901/working/building/REAL250005054673 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054673 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054673/0 /scratch/stefan/7922901/working/building/REAL250005054673 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/820 `/scratch/stefan/7922901/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(=O)NC1CC1) `REAL250005054673.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054673 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 69, 136, 170, 201, 201, 201, 201, 201, 201, 201, 201, 6, 27, 6, 6, 1, 1, 1, 1, 72, 72, 72, 136, 136, 170, 170, 201, 201, 6, 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: 849 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054673 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 79, 123, 123, 155, 155, 155, 201, 201, 79, 79, 79, 44, 44, 24, 24, 4, 1, 155, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054673 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054673 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054673/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054673 Building REAL250005054674 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054674' /scratch/stefan/7922901/working/building/REAL250005054674 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054674 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054674/0 /scratch/stefan/7922901/working/building/REAL250005054674 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/821 `/scratch/stefan/7922901/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC(N)=NN1) `REAL250005054674.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054674 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC(N)=NN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 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: [33, 11, 33, 88, 115, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 33, 88, 88, 115, 115, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 752 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: REAL250005054674 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC(N)=NN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 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: [73, 35, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 73, 139, 139, 201, 201, 201, 201, 201, 73, 73, 73, 35, 35, 22, 22, 4, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 576 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054674 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054674 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054674/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054674 Building REAL250005054675 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054675' /scratch/stefan/7922901/working/building/REAL250005054675 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054675 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054675/0 /scratch/stefan/7922901/working/building/REAL250005054675 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/822 `/scratch/stefan/7922901/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCSC1) `REAL250005054675.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054675 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCSC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 6, 19, 66, 107, 199, 199, 199, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 19, 19, 19, 66, 66, 107, 107, 199, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 776 number of broken/clashed sets: 86 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054675 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCSC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 45, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 87, 169, 169, 201, 201, 201, 201, 87, 87, 87, 45, 45, 27, 27, 7, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 688 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054675 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054675 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054675/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054675 Building REAL250005054676 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054676' /scratch/stefan/7922901/working/building/REAL250005054676 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054676 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054676/0 /scratch/stefan/7922901/working/building/REAL250005054676 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/823 `/scratch/stefan/7922901/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCO1) `REAL250005054676.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054676 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 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: [13, 7, 13, 33, 50, 100, 100, 100, 105, 105, 105, 105, 105, 1, 7, 1, 1, 1, 1, 13, 13, 13, 33, 33, 50, 50, 100, 105, 1, 1, 1, 1, 1] 105 rigid atoms, others: [32, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 375 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: REAL250005054676 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 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: [80, 49, 29, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 80, 99, 99, 105, 105, 105, 80, 80, 80, 49, 49, 29, 29, 6, 1, 105, 105, 105, 105, 105] 105 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 400 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054676 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054676 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054676/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054676 Building REAL250005054677 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054677' /scratch/stefan/7922901/working/building/REAL250005054677 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054677 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054677/0 /scratch/stefan/7922901/working/building/REAL250005054677 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/824 `/scratch/stefan/7922901/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054677.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054677 none CCCC(O)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 573 conformations in input total number of sets (complete confs): 573 using faster count positions algorithm for large data unique positions, atoms: [191, 185, 153, 96, 153, 57, 46, 57, 28, 46, 19, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 191, 191, 191, 191, 191, 185, 185, 153, 459, 96, 96, 46, 46, 46, 28, 28, 19, 19, 4, 1] 573 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: 1358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054677 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054677 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054677/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054677 Building REAL250005054678 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054678' /scratch/stefan/7922901/working/building/REAL250005054678 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054678 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054678/0 /scratch/stefan/7922901/working/building/REAL250005054678 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/825 `/scratch/stefan/7922901/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)CC#N) `REAL250005054678.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054678 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)CC#N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [47, 27, 18, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 47, 47, 47, 73, 73, 73, 93, 93, 47, 47, 47, 27, 27, 18, 18, 6, 1, 73, 73, 73, 73, 73, 73, 92, 93] 93 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 457 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054678 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054678 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054678/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054678 Building REAL250005054679 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054679' /scratch/stefan/7922901/working/building/REAL250005054679 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054679 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054679/0 /scratch/stefan/7922901/working/building/REAL250005054679 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/826 `/scratch/stefan/7922901/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(Cl)CC1) `REAL250005054679.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054679 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(Cl)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 6, 14, 51, 89, 179, 179, 179, 184, 184, 184, 184, 184, 1, 6, 1, 1, 1, 1, 14, 14, 14, 51, 51, 89, 89, 179, 184, 1, 1, 1, 1] 184 rigid atoms, others: [13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 695 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: REAL250005054679 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(Cl)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [97, 51, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 97, 151, 151, 184, 184, 184, 97, 97, 97, 51, 51, 28, 28, 8, 1, 184, 184, 184, 184] 184 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 664 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054679 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054679 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054679/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054679 Building REAL250005054680 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054680' /scratch/stefan/7922901/working/building/REAL250005054680 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054680 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054680/0 /scratch/stefan/7922901/working/building/REAL250005054680 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/827 `/scratch/stefan/7922901/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCCO1) `REAL250005054680.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054680 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [27, 11, 27, 75, 109, 195, 195, 195, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 27, 27, 27, 75, 75, 109, 109, 195, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 730 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: REAL250005054680 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [102, 46, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 101, 179, 180, 201, 201, 201, 201, 102, 102, 102, 46, 46, 28, 28, 8, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 638 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054680 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054680 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054680/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054680 Building REAL250005054681 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054681' /scratch/stefan/7922901/working/building/REAL250005054681 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054681 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054681/0 /scratch/stefan/7922901/working/building/REAL250005054681 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/828 `/scratch/stefan/7922901/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CO)COC1) `REAL250005054681.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054681 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CO)COC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 14, 22, 48, 48, 48, 55, 55, 55, 55, 55, 1, 3, 1, 1, 8, 1, 1, 1, 5, 5, 5, 14, 14, 22, 22, 48, 55, 8, 8, 24, 1, 1, 1, 1] 168 rigid atoms, others: [33, 34, 35, 36, 13, 15, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 233 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054681 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CO)COC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [45, 30, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 45, 55, 55, 55, 56, 55, 55, 55, 45, 45, 45, 30, 30, 20, 20, 5, 1, 56, 56, 168, 55, 55, 55, 55] 168 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 378 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054681 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054681 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054681/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054681 Building REAL250005054682 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054682' /scratch/stefan/7922901/working/building/REAL250005054682 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054682 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054682/0 /scratch/stefan/7922901/working/building/REAL250005054682 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/829 `/scratch/stefan/7922901/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054682.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054682 none CC(C)=CCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 165, 128, 69, 55, 69, 29, 55, 18, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 165, 165, 129, 129, 55, 55, 55, 29, 29, 18, 18, 6, 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: 861 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054682 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054682 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054682/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054682 Building REAL250005054683 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054683' /scratch/stefan/7922901/working/building/REAL250005054683 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054683 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054683/0 /scratch/stefan/7922901/working/building/REAL250005054683 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/830 `/scratch/stefan/7922901/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1COC1) `REAL250005054683.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054683 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1COC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 8, 25, 75, 105, 197, 197, 197, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 25, 25, 25, 75, 75, 105, 105, 197, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 737 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: REAL250005054683 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1COC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 52, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 111, 163, 163, 201, 201, 201, 111, 111, 111, 52, 52, 30, 30, 8, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 719 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054683 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054683 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054683/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054683 Building REAL250005054684 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054684' /scratch/stefan/7922901/working/building/REAL250005054684 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054684 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054684/0 /scratch/stefan/7922901/working/building/REAL250005054684 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/831 `/scratch/stefan/7922901/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005054684.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054684 none CC1CCC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 111, 76, 111, 43, 76, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 76, 76, 76, 43, 43, 28, 28, 9, 1] 125 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: 440 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: REAL250005054684 none CC1CCC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 48, 69, 120, 120, 120, 125, 125, 125, 125, 125, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 48, 48, 69, 69, 120, 125] 125 rigid atoms, others: [0, 1, 2, 3, 4, 5, 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: 458 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054684 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054684 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054684/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054684 Building REAL250005054685 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054685' /scratch/stefan/7922901/working/building/REAL250005054685 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054685 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054685/0 /scratch/stefan/7922901/working/building/REAL250005054685 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/832 `/scratch/stefan/7922901/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NNC=C1N) `REAL250005054685.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054685 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NNC=C1N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 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: [31, 10, 31, 67, 102, 193, 193, 193, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 31, 67, 67, 102, 102, 193, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 720 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054685 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NNC=C1N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 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: [93, 44, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 91, 185, 185, 201, 201, 201, 201, 201, 93, 93, 93, 44, 44, 26, 26, 7, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 653 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054685 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054685 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054685/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054685 Building REAL250005054686 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054686' /scratch/stefan/7922901/working/building/REAL250005054686 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054686 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054686/0 /scratch/stefan/7922901/working/building/REAL250005054686 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/833 `/scratch/stefan/7922901/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CCO) `REAL250005054686.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054686 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CCO NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 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: [95, 54, 28, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 93, 125, 127, 163, 163, 195, 95, 95, 95, 54, 54, 28, 28, 9, 1, 163, 163, 195, 195, 585] 585 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 1382 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054686 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054686 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054686/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054686 Building REAL250005054687 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054687' /scratch/stefan/7922901/working/building/REAL250005054687 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054687 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054687/0 /scratch/stefan/7922901/working/building/REAL250005054687 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/834 `/scratch/stefan/7922901/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=NN1) `REAL250005054687.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054687 none CC1=NC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 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, 115, 69, 115, 47, 69, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 69, 69, 69, 47, 47, 32, 32, 11, 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: 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: REAL250005054687 none CC1=NC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 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, 12, 12, 40, 40, 103, 122, 195, 195, 195, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 40, 40, 40, 103, 103, 122, 122, 195, 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: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054687 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054687/1 /scratch/stefan/7922901/working/building/REAL250005054687 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/835 `/scratch/stefan/7922901/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005054687.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054687 none CC1=NNC(C(=O)N(C)CCNC(=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', '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, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 153, 86, 153, 47, 86, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 86, 86, 86, 47, 47, 30, 30, 9, 1] 155 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: 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: REAL250005054687 none CC1=NNC(C(=O)N(C)CCNC(=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', '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, 1, 8, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 22, 22, 57, 79, 149, 149, 149, 155, 155, 155, 155, 155, 1, 2, 2, 2, 1, 22, 22, 22, 57, 57, 79, 79, 149, 155] 155 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: 585 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054687 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054687 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054687/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054687/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054687 Building REAL250005054688 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054688' /scratch/stefan/7922901/working/building/REAL250005054688 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054688 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054688/0 /scratch/stefan/7922901/working/building/REAL250005054688 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/836 `/scratch/stefan/7922901/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COC(=O)N1) `REAL250005054688.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054688 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 29, 75, 106, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 29, 29, 29, 75, 75, 106, 106, 201, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 752 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: REAL250005054688 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 75, 133, 133, 201, 201, 201, 201, 201, 75, 75, 75, 36, 36, 22, 22, 4, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 571 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054688 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054688/1 /scratch/stefan/7922901/working/building/REAL250005054688 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/837 `/scratch/stefan/7922901/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COC(=O)[N-]1) `REAL250005054688.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054688 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 17, 23, 27, 27, 27, 37, 37, 37, 37, 37, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 17, 17, 23, 23, 27, 37, 1] 37 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054688 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 5, 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: [19, 15, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 19, 35, 35, 37, 37, 37, 37, 37, 19, 19, 19, 15, 15, 10, 10, 3, 1, 37] 37 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054688 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054688 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054688/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054688/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054688 Building REAL250005054689 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054689' /scratch/stefan/7922901/working/building/REAL250005054689 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054689 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054689/0 /scratch/stefan/7922901/working/building/REAL250005054689 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/838 `/scratch/stefan/7922901/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054689.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054689 none CC=CC(O)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 351 conformations in input total number of sets (complete confs): 351 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 92, 74, 92, 58, 74, 38, 58, 23, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 92, 276, 58, 58, 58, 38, 38, 23, 23, 6, 1] 351 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: 753 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054689 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054689 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054689/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054689 Building REAL250005054690 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054690' /scratch/stefan/7922901/working/building/REAL250005054690 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054690 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054690/0 /scratch/stefan/7922901/working/building/REAL250005054690 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/839 `/scratch/stefan/7922901/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054690.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054690 none CCCC[C@H](C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 175, 115, 65, 115, 115, 48, 65, 33, 48, 21, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 184, 186, 178, 178, 115, 115, 115, 48, 48, 48, 33, 33, 21, 21, 5, 1] 201 rigid atoms, others: [42, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 957 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054690 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054690 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054690/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054690 Building REAL250005054691 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054691' /scratch/stefan/7922901/working/building/REAL250005054691 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054691 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054691/0 /scratch/stefan/7922901/working/building/REAL250005054691 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/840 `/scratch/stefan/7922901/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005054691.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054691 none C[C@@H](C(=O)N(C)CCNC(=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', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 14, 13, 13, 12, 13, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 12, 12, 12, 12, 6, 1, 14, 14, 14, 14, 14, 14] 14 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: 53 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054691 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054691/1 /scratch/stefan/7922901/working/building/REAL250005054691 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/841 `/scratch/stefan/7922901/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)N(C)C) `REAL250005054691.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005054691 none C[C@@H](C(=O)N(C)CCNC(=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', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [101, 83, 101, 59, 83, 34, 59, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 101, 102, 102, 101, 101, 101, 59, 59, 59, 34, 34, 23, 23, 7, 1, 102, 102, 102, 102, 102, 102] 102 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: 397 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054691 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054691 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054691/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054691/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054691 Building REAL250005054692 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054692' /scratch/stefan/7922901/working/building/REAL250005054692 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054692 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054692/0 /scratch/stefan/7922901/working/building/REAL250005054692 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/842 `/scratch/stefan/7922901/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054692.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054692 none CCC=C(F)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 133, 133, 85, 133, 56, 85, 29, 56, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 133, 56, 56, 56, 29, 29, 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: 864 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054692 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054692 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054692/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054692 Building REAL250005054693 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054693' /scratch/stefan/7922901/working/building/REAL250005054693 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054693 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054693/0 /scratch/stefan/7922901/working/building/REAL250005054693 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/843 `/scratch/stefan/7922901/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054693.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054693 none CCC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 168, 168, 101, 68, 101, 38, 68, 24, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 168, 168, 68, 68, 68, 38, 38, 24, 24, 8, 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: 805 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054693 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054693 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054693/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054693 Building REAL250005054694 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054694' /scratch/stefan/7922901/working/building/REAL250005054694 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054694 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054694/0 /scratch/stefan/7922901/working/building/REAL250005054694 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/844 `/scratch/stefan/7922901/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CNC(=O)C1) `REAL250005054694.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054694 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CNC(=O)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 23, 68, 106, 197, 197, 197, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 23, 23, 23, 68, 68, 106, 106, 197, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 762 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054694 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CNC(=O)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 43, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 90, 164, 164, 201, 201, 201, 201, 201, 92, 92, 92, 43, 43, 26, 26, 6, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 706 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054694 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054694 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054694/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054694 Building REAL250005054695 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054695' /scratch/stefan/7922901/working/building/REAL250005054695 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054695 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054695/0 /scratch/stefan/7922901/working/building/REAL250005054695 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/845 `/scratch/stefan/7922901/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NON=C1N) `REAL250005054695.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054695 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NON=C1N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 30, 76, 113, 201, 201, 201, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 76, 76, 113, 113, 201, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 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]) 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: REAL250005054695 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NON=C1N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 42, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 96, 183, 183, 201, 201, 201, 201, 201, 96, 96, 96, 42, 42, 23, 23, 5, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 641 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054695 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054695 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054695/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054695 Building REAL250005054696 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054696' /scratch/stefan/7922901/working/building/REAL250005054696 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054696 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054696/0 /scratch/stefan/7922901/working/building/REAL250005054696 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/846 `/scratch/stefan/7922901/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CNC(=O)N1) `REAL250005054696.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054696 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CNC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 7, 6, 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: [25, 7, 25, 73, 111, 196, 196, 196, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 73, 73, 111, 111, 196, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 779 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054696 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CNC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 7, 6, 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: [98, 47, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 98, 174, 174, 201, 201, 201, 201, 201, 201, 98, 98, 98, 47, 47, 27, 27, 7, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 700 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054696 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054696 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054696/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054696 Building REAL250005054697 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054697' /scratch/stefan/7922901/working/building/REAL250005054697 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054697 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054697/0 /scratch/stefan/7922901/working/building/REAL250005054697 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/847 `/scratch/stefan/7922901/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CS1) `REAL250005054697.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054697 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 21, 74, 108, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 21, 21, 21, 74, 74, 108, 108, 201, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 768 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: REAL250005054697 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CN=CS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 79, 144, 144, 201, 201, 201, 201, 79, 79, 79, 42, 42, 24, 24, 4, 1, 201, 200] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 610 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054697 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054697 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054697/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054697 Building REAL250005054698 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054698' /scratch/stefan/7922901/working/building/REAL250005054698 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054698 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054698/0 /scratch/stefan/7922901/working/building/REAL250005054698 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/848 `/scratch/stefan/7922901/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCN=[N+]=[N-]) `REAL250005054698.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054698 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCN=[N+]=[N-] NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'N.2', 'N.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 63, 97, 97, 99, 121, 201, 201, 63, 63, 63, 28, 28, 18, 18, 4, 1, 99, 99, 121, 121] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 593 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054698 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054698 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054698/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054698 Building REAL250005054699 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054699' /scratch/stefan/7922901/working/building/REAL250005054699 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054699 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054699/0 /scratch/stefan/7922901/working/building/REAL250005054699 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/849 `/scratch/stefan/7922901/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054699.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054699 none C#CCOCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 140, 89, 61, 55, 61, 33, 55, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 89, 89, 55, 55, 55, 33, 33, 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: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054699 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054699 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054699/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054699 Building REAL250005054700 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054700' /scratch/stefan/7922901/working/building/REAL250005054700 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054700 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054700/0 /scratch/stefan/7922901/working/building/REAL250005054700 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/850 `/scratch/stefan/7922901/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NN=CO1) `REAL250005054700.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054700 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NN=CO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 26, 50, 102, 134, 201, 201, 201, 201, 201, 201, 201, 201, 4, 26, 1, 1, 1, 1, 1, 1, 51, 51, 51, 102, 102, 134, 134, 201, 201, 4, 4, 1] 201 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 785 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054700 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=NN=CO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 28, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 54, 96, 96, 163, 201, 201, 201, 201, 54, 54, 54, 28, 28, 19, 19, 4, 1, 163, 163, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 700 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054700 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054700 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054700/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054700 Building REAL250005054701 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054701' /scratch/stefan/7922901/working/building/REAL250005054701 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054701 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054701/0 /scratch/stefan/7922901/working/building/REAL250005054701 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/851 `/scratch/stefan/7922901/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCS1) `REAL250005054701.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054701 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 62, 91, 160, 160, 160, 165, 165, 165, 165, 165, 1, 6, 1, 1, 1, 1, 1, 21, 21, 21, 62, 62, 91, 91, 160, 165, 1, 1, 1, 1, 1, 1, 1] 165 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 629 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: REAL250005054701 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCCS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [84, 42, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 84, 147, 147, 165, 165, 165, 165, 84, 84, 84, 42, 42, 27, 27, 8, 1, 165, 165, 165, 165, 165, 165, 165] 165 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 557 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054701 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054701 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054701/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054701 Building REAL250005054702 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054702' /scratch/stefan/7922901/working/building/REAL250005054702 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054702 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054702/0 /scratch/stefan/7922901/working/building/REAL250005054702 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/852 `/scratch/stefan/7922901/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054702.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054702 none COC(C)(C)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 169, 126, 167, 168, 52, 48, 52, 30, 48, 21, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 175, 175, 175, 169, 169, 169, 169, 169, 169, 127, 127, 48, 48, 48, 30, 30, 21, 21, 4, 1] 175 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: 801 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054702 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054702 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054702/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054702 Building REAL250005054703 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054703' /scratch/stefan/7922901/working/building/REAL250005054703 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054703 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054703/0 /scratch/stefan/7922901/working/building/REAL250005054703 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/853 `/scratch/stefan/7922901/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054703.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054703 none CC(O)CCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [56, 45, 56, 38, 17, 17, 17, 15, 17, 9, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 168, 49, 49, 38, 38, 17, 17, 17, 15, 15, 9, 9, 4, 1] 168 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: 459 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054703 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054703 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054703/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054703 Building REAL250005054704 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054704' /scratch/stefan/7922901/working/building/REAL250005054704 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054704 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054704/0 /scratch/stefan/7922901/working/building/REAL250005054704 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/854 `/scratch/stefan/7922901/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=CC=C1) `REAL250005054704.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054704 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=CC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [34, 15, 34, 71, 91, 180, 180, 180, 180, 180, 180, 180, 180, 3, 15, 1, 1, 1, 1, 1, 1, 35, 35, 35, 71, 71, 91, 91, 180, 180, 3, 3, 1, 1, 1, 1] 180 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 650 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054704 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=CC=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 34, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 68, 124, 124, 200, 201, 201, 201, 201, 68, 68, 68, 34, 34, 19, 19, 4, 1, 200, 200, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 774 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054704 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054704 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054704/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054704 Building REAL250005054705 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054705' /scratch/stefan/7922901/working/building/REAL250005054705 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054705 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054705/0 /scratch/stefan/7922901/working/building/REAL250005054705 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/855 `/scratch/stefan/7922901/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054705.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054705 none C#CCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 143, 141, 82, 54, 82, 37, 54, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 144, 144, 144, 142, 142, 54, 54, 54, 37, 37, 22, 22, 4, 1] 144 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: 583 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054705 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054705 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054705/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054705 Building REAL250005054706 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054706' /scratch/stefan/7922901/working/building/REAL250005054706 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054706 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054706/0 /scratch/stefan/7922901/working/building/REAL250005054706 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/856 `/scratch/stefan/7922901/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005054706.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054706 none CC(=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [192, 192, 121, 74, 121, 42, 74, 24, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 192, 201, 201, 192, 192, 192, 192, 74, 74, 74, 42, 42, 24, 24, 5, 1, 201, 201, 201, 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, 38, 39, 40]) total number of confs: 756 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054706 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054706 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054706/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054706 Building REAL250005054707 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054707' /scratch/stefan/7922901/working/building/REAL250005054707 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054707 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054707/0 /scratch/stefan/7922901/working/building/REAL250005054707 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/857 `/scratch/stefan/7922901/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(CC(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054707.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054707 none COC1(CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [190, 182, 136, 66, 61, 66, 40, 61, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 182, 182, 190, 190, 190, 136, 136, 61, 61, 61, 40, 40, 23, 23, 4, 1, 182, 182, 182, 182] 190 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: 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: REAL250005054707 none COC1(CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 9, 33, 33, 40, 40, 95, 118, 175, 175, 175, 182, 182, 182, 182, 182, 1, 1, 6, 6, 6, 9, 9, 40, 40, 40, 95, 95, 118, 118, 175, 182, 1, 1, 1, 1] 190 rigid atoms, others: [1, 2, 3, 36, 37, 35, 19, 20, 38] set([0, 4, 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: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054707 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054707 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054707/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054707 Building REAL250005054708 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054708' /scratch/stefan/7922901/working/building/REAL250005054708 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054708 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054708/0 /scratch/stefan/7922901/working/building/REAL250005054708 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/858 `/scratch/stefan/7922901/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054708.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054708 none CC[C@H](C)[C@H](O)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 7, 5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 453 conformations in input total number of sets (complete confs): 453 using faster count positions algorithm for large data unique positions, atoms: [151, 145, 121, 145, 145, 83, 121, 121, 61, 83, 39, 61, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 145, 145, 145, 363, 61, 61, 61, 39, 39, 24, 24, 7, 1] 453 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: 1050 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054708 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054708 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054708/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054708 Building REAL250005054709 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054709' /scratch/stefan/7922901/working/building/REAL250005054709 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054709 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054709/0 /scratch/stefan/7922901/working/building/REAL250005054709 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/859 `/scratch/stefan/7922901/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054709.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054709 none CC=CC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 137, 137, 92, 57, 92, 35, 57, 24, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 145, 137, 137, 57, 57, 57, 35, 35, 24, 24, 6, 1] 145 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: 518 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054709 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054709 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054709/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054709 Building REAL250005054710 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054710' /scratch/stefan/7922901/working/building/REAL250005054710 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054710 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054710/0 /scratch/stefan/7922901/working/building/REAL250005054710 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/860 `/scratch/stefan/7922901/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC=NN1C) `REAL250005054710.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054710 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC=NN1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 26, 62, 94, 199, 199, 199, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 26, 62, 62, 94, 94, 199, 201, 1, 2, 2, 2] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) 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: REAL250005054710 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC=NN1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 105, 187, 187, 201, 201, 201, 201, 201, 105, 105, 105, 46, 46, 26, 26, 6, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054710 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054710 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054710/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054710 Building REAL250005054711 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054711' /scratch/stefan/7922901/working/building/REAL250005054711 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054711 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054711/0 /scratch/stefan/7922901/working/building/REAL250005054711 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/861 `/scratch/stefan/7922901/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CC[C@@H](O)C1) `REAL250005054711.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054711 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CC[C@@H](O)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 63, 101, 195, 195, 195, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 63, 63, 101, 101, 195, 201, 1, 1, 1, 1, 6, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 757 number of broken/clashed sets: 141 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054711 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CC[C@@H](O)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [82, 40, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 82, 158, 158, 201, 201, 201, 201, 201, 201, 201, 82, 82, 82, 40, 40, 23, 23, 6, 1, 201, 201, 201, 201, 603, 201, 201] 603 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1296 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054711 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054711 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054711/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054711 Building REAL250005054712 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054712' /scratch/stefan/7922901/working/building/REAL250005054712 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054712 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054712/0 /scratch/stefan/7922901/working/building/REAL250005054712 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/862 `/scratch/stefan/7922901/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CC=CCC1) `REAL250005054712.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054712 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CC=CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 55, 98, 197, 197, 197, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 55, 55, 98, 98, 197, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 757 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054712 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CC=CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 69, 154, 154, 201, 201, 201, 201, 201, 201, 70, 70, 70, 35, 35, 22, 22, 5, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 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: 692 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054712 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054712 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054712/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054712 Building REAL250005054713 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054713' /scratch/stefan/7922901/working/building/REAL250005054713 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054713 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054713/0 /scratch/stefan/7922901/working/building/REAL250005054713 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/863 `/scratch/stefan/7922901/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054713.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054713 none COCC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 120, 120, 52, 38, 52, 24, 38, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 120, 120, 38, 38, 38, 24, 24, 17, 17, 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054713 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054713 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054713/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054713 Building REAL250005054714 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054714' /scratch/stefan/7922901/working/building/REAL250005054714 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054714 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054714/0 /scratch/stefan/7922901/working/building/REAL250005054714 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/864 `/scratch/stefan/7922901/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC2CC2C1) `REAL250005054714.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054714 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC2CC2C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 62, 94, 193, 193, 193, 201, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 62, 62, 94, 94, 193, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 746 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054714 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC2CC2C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 46, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 98, 165, 165, 201, 201, 201, 201, 201, 98, 98, 98, 46, 46, 26, 26, 7, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 691 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054714 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054714 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054714/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054714 Building REAL250005054715 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054715' /scratch/stefan/7922901/working/building/REAL250005054715 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054715 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054715/0 /scratch/stefan/7922901/working/building/REAL250005054715 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/865 `/scratch/stefan/7922901/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(CC(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054715.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054715 none CC1CN(CC(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 93, 69, 93, 33, 69, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126, 126, 126, 69, 69, 69, 33, 33, 20, 20, 4, 1, 126, 126] 126 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: 516 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054715 none CC1CN(CC(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 16, 16, 27, 27, 62, 75, 126, 126, 126, 126, 126, 126, 126, 126, 1, 2, 2, 2, 1, 1, 1, 6, 6, 27, 27, 27, 62, 62, 75, 75, 126, 126, 1, 1] 126 rigid atoms, others: [0, 1, 2, 3, 4, 38, 39, 20, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 482 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054715 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054715/1 /scratch/stefan/7922901/working/building/REAL250005054715 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/866 `/scratch/stefan/7922901/working/3D/866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C[NH+](CC(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054715.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054715 none CC1C[NH+](CC(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 27, 19, 19, 19, 19, 19, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 25, 25, 19, 19, 19, 19, 19, 18, 18, 6, 1, 27, 27] 27 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: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054715 none CC1C[NH+](CC(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 22, 22, 27, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 1, 1, 1, 6, 6, 20, 20, 20, 22, 22, 22, 22, 27, 27, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 40, 21, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054715 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054715 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054715/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054715/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054715 Building REAL250005054716 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054716' /scratch/stefan/7922901/working/building/REAL250005054716 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054716 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054716/0 /scratch/stefan/7922901/working/building/REAL250005054716 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/867 `/scratch/stefan/7922901/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054716.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054716 none CCC(C)(O)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 363 conformations in input total number of sets (complete confs): 363 using faster count positions algorithm for large data unique positions, atoms: [121, 93, 93, 93, 93, 63, 93, 33, 63, 22, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 93, 93, 93, 279, 63, 63, 63, 33, 33, 22, 22, 7, 1] 363 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: 771 number of broken/clashed sets: 134 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054716 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054716 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054716/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054716 Building REAL250005054717 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054717' /scratch/stefan/7922901/working/building/REAL250005054717 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054717 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054717/0 /scratch/stefan/7922901/working/building/REAL250005054717 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/868 `/scratch/stefan/7922901/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054717.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054717 none C#CCC(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 135, 94, 135, 66, 94, 38, 66, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 167, 167, 167, 135, 135, 135, 135, 66, 66, 66, 38, 38, 22, 22, 4, 1] 167 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: 767 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054717 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054717 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054717/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054717 Building REAL250005054718 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054718' /scratch/stefan/7922901/working/building/REAL250005054718 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054718 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054718/0 /scratch/stefan/7922901/working/building/REAL250005054718 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/869 `/scratch/stefan/7922901/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054718.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054718 none C=CC(O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 420 conformations in input total number of sets (complete confs): 420 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 107, 140, 70, 107, 41, 70, 23, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 420, 70, 70, 70, 41, 41, 23, 23, 6, 1] 420 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: 980 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054718 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054718 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054718/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054718 Building REAL250005054719 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054719' /scratch/stefan/7922901/working/building/REAL250005054719 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054719 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054719/0 /scratch/stefan/7922901/working/building/REAL250005054719 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/870 `/scratch/stefan/7922901/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCN=[N+]=[N-]) `REAL250005054719.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054719 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCN=[N+]=[N-] NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 21, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 37, 47, 47, 51, 60, 109, 201, 201, 37, 37, 37, 21, 21, 12, 12, 4, 1, 51, 51, 60, 60, 109, 109] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054719 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054719 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054719/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054719 Building REAL250005054720 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054720' /scratch/stefan/7922901/working/building/REAL250005054720 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054720 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054720/0 /scratch/stefan/7922901/working/building/REAL250005054720 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/871 `/scratch/stefan/7922901/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1OCC1(C)C) `REAL250005054720.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054720 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1OCC1(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 5, 12, 25, 38, 74, 74, 74, 83, 83, 83, 83, 83, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 25, 25, 38, 38, 74, 83, 1, 1, 1, 2, 2, 2, 2, 2, 2] 83 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 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, 33, 34, 35, 36, 37, 38]) total number of confs: 290 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: REAL250005054720 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1OCC1(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [56, 32, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 56, 80, 80, 83, 83, 83, 83, 83, 56, 56, 56, 32, 32, 20, 20, 8, 1, 83, 83, 83, 83, 83, 83, 83, 83, 83] 83 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 297 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054720 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054720 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054720/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054720 Building REAL250005054721 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054721' /scratch/stefan/7922901/working/building/REAL250005054721 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054721 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054721/0 /scratch/stefan/7922901/working/building/REAL250005054721 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/872 `/scratch/stefan/7922901/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C12CC1CC2) `REAL250005054721.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054721 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C12CC1CC2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 35, 59, 120, 120, 120, 126, 126, 126, 126, 126, 1, 4, 1, 1, 1, 1, 1, 9, 9, 9, 35, 34, 59, 59, 120, 126, 1, 1, 1, 1, 1, 1, 1] 126 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005054721 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C12CC1CC2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [79, 42, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 79, 121, 121, 126, 126, 126, 126, 79, 79, 79, 42, 42, 26, 26, 8, 1, 126, 126, 126, 126, 126, 126, 126] 126 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054721 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054721 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054721/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054721 Building REAL250005054722 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054722' /scratch/stefan/7922901/working/building/REAL250005054722 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054722 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054722/0 /scratch/stefan/7922901/working/building/REAL250005054722 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/873 `/scratch/stefan/7922901/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054722.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054722 none CCCC(C)=CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 128, 128, 128, 76, 58, 76, 35, 58, 21, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 198, 198, 128, 128, 128, 128, 58, 58, 58, 35, 35, 21, 21, 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: 879 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054722 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054722 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054722/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054722 Building REAL250005054723 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054723' /scratch/stefan/7922901/working/building/REAL250005054723 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054723 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054723/0 /scratch/stefan/7922901/working/building/REAL250005054723 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/874 `/scratch/stefan/7922901/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054723.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054723 none C=C[C@H](C)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 117, 151, 151, 66, 57, 66, 33, 57, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 151, 118, 118, 57, 57, 57, 33, 33, 18, 18, 4, 1] 151 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: 665 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054723 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054723 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054723/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054723 Building REAL250005054724 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054724' /scratch/stefan/7922901/working/building/REAL250005054724 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054724 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054724/0 /scratch/stefan/7922901/working/building/REAL250005054724 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/875 `/scratch/stefan/7922901/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CC1CC1) `REAL250005054724.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054724 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 48, 79, 138, 162, 201, 201, 201, 201, 201, 201, 201, 201, 10, 47, 10, 1, 1, 1, 1, 79, 79, 79, 138, 138, 162, 162, 201, 201, 10, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 760 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: REAL250005054724 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 38, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 106, 106, 157, 157, 201, 201, 65, 65, 65, 38, 38, 18, 18, 4, 1, 157, 157, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 735 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054724 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054724 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054724/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054724 Building REAL250005054725 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054725' /scratch/stefan/7922901/working/building/REAL250005054725 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054725 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054725/0 /scratch/stefan/7922901/working/building/REAL250005054725 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/876 `/scratch/stefan/7922901/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C=NO1) `REAL250005054725.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054725 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 141, 74, 141, 39, 74, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 74, 74, 74, 39, 39, 22, 22, 6, 1, 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]) total number of confs: 579 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: REAL250005054725 none CC1=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 26, 26, 69, 101, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 26, 26, 26, 69, 69, 101, 101, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 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: 758 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054725 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054725 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054725/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054725 Building REAL250005054726 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054726' /scratch/stefan/7922901/working/building/REAL250005054726 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054726 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054726/0 /scratch/stefan/7922901/working/building/REAL250005054726 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/877 `/scratch/stefan/7922901/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054726.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054726 none CC(C)CC(=O)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 198, 201, 134, 83, 134, 67, 83, 39, 67, 25, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 198, 198, 67, 67, 67, 39, 39, 25, 25, 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: 874 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054726 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054726 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054726/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054726 Building REAL250005054727 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054727' /scratch/stefan/7922901/working/building/REAL250005054727 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054727 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054727/0 /scratch/stefan/7922901/working/building/REAL250005054727 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/878 `/scratch/stefan/7922901/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1(C#N)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054727.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054727 none CC1CC1(C#N)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 38, 56, 24, 38, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 38, 38, 38, 24, 24, 17, 17, 6, 1] 56 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: 196 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: REAL250005054727 none CC1CC1(C#N)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 6, 6, 17, 27, 54, 54, 54, 56, 56, 56, 56, 56, 2, 2, 2, 1, 1, 1, 6, 6, 6, 17, 17, 27, 27, 54, 56] 56 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 211 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054727 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054727 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054727/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054727 Building REAL250005054728 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054728' /scratch/stefan/7922901/working/building/REAL250005054728 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054728 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054728/0 /scratch/stefan/7922901/working/building/REAL250005054728 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/879 `/scratch/stefan/7922901/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C#N)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054728.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054728 none CCC(C#N)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [146, 127, 97, 127, 127, 66, 97, 38, 66, 21, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 152, 127, 66, 66, 66, 38, 38, 21, 21, 5, 1] 152 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: 720 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054728 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054728 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054728/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054728 Building REAL250005054729 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054729' /scratch/stefan/7922901/working/building/REAL250005054729 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054729 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054729/0 /scratch/stefan/7922901/working/building/REAL250005054729 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/880 `/scratch/stefan/7922901/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CNC(=O)O1) `REAL250005054729.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054729 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CNC(=O)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 7, 6, 3, 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: [18, 7, 18, 44, 65, 114, 114, 114, 120, 120, 120, 120, 120, 1, 7, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 44, 44, 65, 65, 114, 120, 1, 1, 1] 120 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 431 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: REAL250005054729 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CNC(=O)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 7, 6, 3, 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: [66, 33, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 66, 112, 112, 120, 120, 120, 120, 120, 120, 66, 66, 66, 33, 33, 23, 23, 7, 1, 120, 120, 120] 120 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 403 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054729 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054729 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054729/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054729 Building REAL250005054730 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054730' /scratch/stefan/7922901/working/building/REAL250005054730 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054730 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054730/0 /scratch/stefan/7922901/working/building/REAL250005054730 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/881 `/scratch/stefan/7922901/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1C2CCC21) `REAL250005054730.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054730 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1C2CCC21 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 15, 45, 67, 130, 130, 130, 138, 138, 138, 138, 138, 1, 7, 1, 1, 1, 1, 1, 15, 15, 15, 45, 45, 67, 67, 130, 138, 1, 1, 1, 1, 1, 1, 1] 138 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 493 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054730 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1C2CCC21 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [70, 32, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 68, 110, 110, 138, 138, 138, 138, 70, 70, 70, 32, 32, 22, 22, 9, 1, 138, 138, 138, 138, 138, 138, 138] 138 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054730 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054730 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054730/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054730 Building REAL250005054731 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054731' /scratch/stefan/7922901/working/building/REAL250005054731 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054731 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054731/0 /scratch/stefan/7922901/working/building/REAL250005054731 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/882 `/scratch/stefan/7922901/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054731.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054731 none C=C1CCC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 55, 44, 55, 26, 44, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 44, 44, 44, 26, 26, 16, 16, 6, 1] 68 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: 260 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: REAL250005054731 none C=C1CCC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 12, 12, 24, 36, 66, 66, 66, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 24, 24, 36, 36, 66, 68] 68 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 248 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054731 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054731 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054731/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054731 Building REAL250005054732 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054732' /scratch/stefan/7922901/working/building/REAL250005054732 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054732 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054732/0 /scratch/stefan/7922901/working/building/REAL250005054732 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/883 `/scratch/stefan/7922901/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)[C@H]1C) `REAL250005054732.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054732 none C[C@H]1C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 96, 60, 96, 39, 60, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 150, 150, 60, 60, 60, 39, 39, 24, 24, 8, 1, 150, 150, 150] 150 rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 532 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: REAL250005054732 none C[C@H]1C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 23, 23, 58, 77, 145, 145, 145, 150, 150, 150, 150, 150, 1, 1, 1, 2, 2, 2, 1, 23, 23, 23, 58, 58, 77, 77, 145, 150, 2, 2, 2] 150 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 547 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054732 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054732 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054732/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054732 Building REAL250005054733 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054733' /scratch/stefan/7922901/working/building/REAL250005054733 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005054733 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054733/0 /scratch/stefan/7922901/working/building/REAL250005054733 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/884 `/scratch/stefan/7922901/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054733.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054733 none CC[N@H+](C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 16, 19, 19, 16, 14, 16, 14, 14, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 19, 19, 19, 16, 16, 14, 14, 14, 14, 14, 12, 12, 4, 1] 20 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: 86 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054733 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054733/1 /scratch/stefan/7922901/working/building/REAL250005054733 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/885 `/scratch/stefan/7922901/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054733.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005054733 none CC[N@@H+](C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 17, 19, 19, 17, 15, 17, 15, 15, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 19, 19, 19, 17, 17, 15, 15, 15, 15, 15, 13, 13, 4, 1] 20 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: 83 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054733 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `2' /scratch/stefan/7922901/working/building/REAL250005054733/2 /scratch/stefan/7922901/working/building/REAL250005054733 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 2 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/886 `/scratch/stefan/7922901/working/3D/886' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054733.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005054733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054733/2/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: REAL250005054733 none CCN(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 86, 74, 86, 60, 55, 60, 42, 55, 27, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 86, 86, 86, 74, 74, 55, 55, 55, 42, 42, 27, 27, 8, 1] 90 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: 379 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054733 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054733 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054733/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054733/1.* 2: /scratch/stefan/7922901/working/building/REAL250005054733/2.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054733 Building REAL250005054734 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054734' /scratch/stefan/7922901/working/building/REAL250005054734 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054734 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054734/0 /scratch/stefan/7922901/working/building/REAL250005054734 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/887 `/scratch/stefan/7922901/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC2(C1)N=N2) `REAL250005054734.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054734 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC2(C1)N=N2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 73, 114, 201, 201, 201, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 27, 27, 27, 73, 73, 114, 114, 201, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 759 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: REAL250005054734 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC2(C1)N=N2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 35, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 74, 157, 157, 201, 201, 201, 201, 201, 74, 74, 74, 35, 35, 18, 18, 4, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 681 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054734 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054734 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054734/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054734 Building REAL250005054735 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054735' /scratch/stefan/7922901/working/building/REAL250005054735 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054735 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054735/0 /scratch/stefan/7922901/working/building/REAL250005054735 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/888 `/scratch/stefan/7922901/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054735.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054735 none CC(O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [53, 49, 53, 42, 49, 26, 42, 18, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 159, 42, 42, 42, 26, 26, 18, 18, 7, 1] 159 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: 371 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054735 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054735 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054735/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054735 Building REAL250005054736 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054736' /scratch/stefan/7922901/working/building/REAL250005054736 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054736 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054736/0 /scratch/stefan/7922901/working/building/REAL250005054736 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/889 `/scratch/stefan/7922901/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054736.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054736 none CC(=O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 92, 125, 69, 92, 36, 69, 25, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 125, 125, 125, 69, 69, 69, 36, 36, 25, 25, 7, 1] 125 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: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054736 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054736 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054736/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054736 Building REAL250005054737 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054737' /scratch/stefan/7922901/working/building/REAL250005054737 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054737 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054737/0 /scratch/stefan/7922901/working/building/REAL250005054737 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/890 `/scratch/stefan/7922901/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNN=C1N) `REAL250005054737.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054737 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNN=C1N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 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: [25, 9, 25, 77, 111, 201, 201, 201, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 77, 77, 111, 111, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 30, 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]) 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: REAL250005054737 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNN=C1N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 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: [75, 36, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 75, 151, 151, 201, 201, 201, 201, 201, 75, 75, 75, 36, 36, 22, 22, 4, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054737 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054737 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054737/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054737 Building REAL250005054738 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054738' /scratch/stefan/7922901/working/building/REAL250005054738 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054738 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054738/0 /scratch/stefan/7922901/working/building/REAL250005054738 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/891 `/scratch/stefan/7922901/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(N)=O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054738.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054738 none CC(NC(N)=O)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 4, 6, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 71, 95, 95, 95, 95, 65, 71, 34, 65, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95, 65, 65, 65, 34, 34, 20, 20, 4, 1] 95 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: 390 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054738 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054738 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054738/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054738 Building REAL250005054739 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054739' /scratch/stefan/7922901/working/building/REAL250005054739 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054739 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054739/0 /scratch/stefan/7922901/working/building/REAL250005054739 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/892 `/scratch/stefan/7922901/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054739.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054739 none CCOC(=O)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 97, 97, 43, 97, 26, 26, 26, 14, 26, 9, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 43, 43, 26, 26, 26, 14, 14, 9, 9, 3, 1] 99 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: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054739 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054739 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054739/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054739 Building REAL250005054740 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054740' /scratch/stefan/7922901/working/building/REAL250005054740 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054740 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054740/0 /scratch/stefan/7922901/working/building/REAL250005054740 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/893 `/scratch/stefan/7922901/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC(=O)N[N-]1) `REAL250005054740.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054740 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC(=O)N[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 23, 32, 36, 36, 36, 46, 46, 46, 46, 46, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 23, 23, 32, 32, 36, 46, 1, 1] 46 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054740 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC(=O)N[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 22, 41, 41, 46, 46, 46, 46, 46, 22, 22, 22, 17, 17, 12, 12, 4, 1, 46, 46] 46 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054740 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054740 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054740/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054740 Building REAL250005054741 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054741' /scratch/stefan/7922901/working/building/REAL250005054741 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054741 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054741/0 /scratch/stefan/7922901/working/building/REAL250005054741 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/894 `/scratch/stefan/7922901/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=CN1) `REAL250005054741.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054741 none CC1=CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 69, 128, 40, 69, 24, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 69, 69, 69, 40, 40, 24, 24, 5, 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: 587 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: REAL250005054741 none CC1=CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7] 0 hydrogens 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, 11, 11, 27, 27, 69, 92, 199, 199, 199, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 27, 27, 27, 69, 69, 92, 92, 199, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 35, 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: 720 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054741 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054741 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054741/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054741 Building REAL250005054742 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054742' /scratch/stefan/7922901/working/building/REAL250005054742 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054742 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054742/0 /scratch/stefan/7922901/working/building/REAL250005054742 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/895 `/scratch/stefan/7922901/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005054742.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054742 none CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 84, 64, 84, 37, 64, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 64, 64, 64, 37, 37, 24, 24, 7, 1, 119, 119, 119, 119, 119, 119] 119 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: 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: REAL250005054742 none CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 17, 17, 43, 63, 109, 111, 109, 119, 119, 119, 119, 119, 1, 1, 1, 2, 2, 2, 17, 17, 17, 43, 43, 63, 63, 111, 119, 1, 1, 1, 1, 1, 1] 119 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 33, 34, 18, 19, 20, 38] 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: 428 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054742 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054742 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054742/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054742 Building REAL250005054743 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054743' /scratch/stefan/7922901/working/building/REAL250005054743 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054743 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054743/0 /scratch/stefan/7922901/working/building/REAL250005054743 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/896 `/scratch/stefan/7922901/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCC#N) `REAL250005054743.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054743 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCC#N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 53, 88, 88, 95, 117, 201, 201, 53, 53, 53, 22, 22, 13, 13, 4, 1, 95, 95, 117, 117, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 931 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054743 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054743 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054743/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054743 Building REAL250005054744 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054744' /scratch/stefan/7922901/working/building/REAL250005054744 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054744 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054744/0 /scratch/stefan/7922901/working/building/REAL250005054744 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/897 `/scratch/stefan/7922901/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C#N)CC1) `REAL250005054744.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054744 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C#N)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 5, 12, 36, 60, 124, 124, 124, 127, 127, 127, 127, 127, 1, 5, 1, 1, 1, 1, 1, 12, 12, 12, 36, 36, 60, 60, 124, 127, 1, 1, 1, 1] 127 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 465 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: REAL250005054744 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C#N)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [77, 43, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 77, 122, 122, 127, 127, 127, 127, 77, 77, 77, 43, 43, 26, 26, 7, 1, 127, 127, 127, 127] 127 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 439 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054744 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054744 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054744/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054744 Building REAL250005054745 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054745' /scratch/stefan/7922901/working/building/REAL250005054745 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054745 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054745/0 /scratch/stefan/7922901/working/building/REAL250005054745 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/898 `/scratch/stefan/7922901/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005054745.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054745 none C=C1CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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 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, 105, 74, 105, 42, 74, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 74, 74, 74, 42, 42, 30, 30, 8, 1, 135, 135] 135 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: 483 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: REAL250005054745 none C=C1CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 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 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, 6, 6, 21, 21, 51, 69, 129, 129, 129, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 21, 21, 21, 51, 51, 69, 69, 129, 135, 1, 1] 135 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 19, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 491 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054745 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054745 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054745/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054745 Building REAL250005054746 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054746' /scratch/stefan/7922901/working/building/REAL250005054746 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054746 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054746/0 /scratch/stefan/7922901/working/building/REAL250005054746 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/899 `/scratch/stefan/7922901/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@]12C[C@H]1[C@H](O)C2) `REAL250005054746.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054746 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@]12C[C@H]1[C@H](O)C2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 372 conformations in input total number of sets (complete confs): 372 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 35, 62, 118, 118, 118, 124, 124, 124, 124, 124, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 35, 35, 62, 62, 118, 124, 1, 1, 3, 1, 1] 372 rigid atoms, others: [32, 33, 35, 36, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 461 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: REAL250005054746 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@]12C[C@H]1[C@H](O)C2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 372 conformations in input total number of sets (complete confs): 372 using faster count positions algorithm for large data unique positions, atoms: [68, 36, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 68, 114, 114, 124, 124, 124, 124, 124, 124, 124, 69, 69, 69, 36, 36, 21, 21, 7, 1, 124, 124, 372, 124, 124] 372 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 800 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054746 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054746 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054746/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054746 Building REAL250005054747 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054747' /scratch/stefan/7922901/working/building/REAL250005054747 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054747 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054747/0 /scratch/stefan/7922901/working/building/REAL250005054747 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/900 `/scratch/stefan/7922901/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C12CC(C1)CO2) `REAL250005054747.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054747 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C12CC(C1)CO2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 20, 66, 103, 200, 200, 200, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 66, 66, 103, 103, 200, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 755 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: REAL250005054747 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C12CC(C1)CO2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 44, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 92, 163, 163, 201, 201, 201, 201, 201, 92, 92, 92, 44, 44, 26, 26, 6, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 615 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054747 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054747 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054747/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054747 Building REAL250005054748 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054748' /scratch/stefan/7922901/working/building/REAL250005054748 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054748 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054748/0 /scratch/stefan/7922901/working/building/REAL250005054748 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/901 `/scratch/stefan/7922901/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054748.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054748 none CCC=CC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 131, 131, 117, 117, 67, 45, 67, 34, 45, 20, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 131, 131, 117, 117, 45, 45, 45, 34, 34, 20, 20, 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: 885 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054748 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054748 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054748/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054748 Building REAL250005054749 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054749' /scratch/stefan/7922901/working/building/REAL250005054749 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054749 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054749/0 /scratch/stefan/7922901/working/building/REAL250005054749 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/902 `/scratch/stefan/7922901/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN(C)C(N)=O) `REAL250005054749.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054749 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN(C)C(N)=O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 4, 6, 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: [13, 9, 6, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 19, 19, 21, 28, 28, 29, 29, 13, 13, 13, 9, 9, 6, 6, 2, 1, 21, 21, 28, 28, 28, 29, 29] 29 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 122 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054749 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054749 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054749/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054749 Building REAL250005054750 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054750' /scratch/stefan/7922901/working/building/REAL250005054750 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054750 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054750/0 /scratch/stefan/7922901/working/building/REAL250005054750 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/903 `/scratch/stefan/7922901/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NNC(=O)[N-]1) `REAL250005054750.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054750 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 18, 26, 32, 32, 32, 50, 50, 50, 50, 50, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 18, 18, 26, 26, 32, 50, 1] 50 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054750 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NNC(=O)[N-]1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 17, 31, 31, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 13, 13, 5, 1, 50] 50 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054750 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054750 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054750/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054750 Building REAL250005054751 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054751' /scratch/stefan/7922901/working/building/REAL250005054751 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054751 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054751/0 /scratch/stefan/7922901/working/building/REAL250005054751 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/904 `/scratch/stefan/7922901/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(F)CC1) `REAL250005054751.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054751 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 7, 13, 46, 67, 135, 135, 135, 139, 139, 139, 139, 139, 1, 7, 1, 1, 1, 1, 13, 13, 13, 46, 46, 67, 67, 135, 139, 1, 1, 1, 1] 139 rigid atoms, others: [13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 508 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054751 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(F)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [79, 40, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 79, 110, 110, 139, 139, 139, 79, 79, 79, 40, 40, 25, 25, 7, 1, 139, 139, 139, 139] 139 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054751 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054751 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054751/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054751 Building REAL250005054752 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054752' /scratch/stefan/7922901/working/building/REAL250005054752 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054752 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054752/0 /scratch/stefan/7922901/working/building/REAL250005054752 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/905 `/scratch/stefan/7922901/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(O)C1CC1) `REAL250005054752.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054752 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(O)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 411 conformations in input total number of sets (complete confs): 411 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 49, 72, 137, 137, 137, 137, 137, 137, 137, 137, 6, 10, 1, 6, 6, 1, 1, 1, 21, 21, 21, 49, 49, 72, 72, 137, 137, 6, 6, 6, 18, 1, 1, 1, 1, 1] 411 rigid atoms, others: [34, 35, 36, 37, 38, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 544 number of broken/clashed sets: 187 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054752 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(O)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 411 conformations in input total number of sets (complete confs): 411 using faster count positions algorithm for large data unique positions, atoms: [64, 32, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 64, 98, 98, 114, 114, 114, 137, 137, 64, 64, 64, 32, 32, 19, 19, 5, 1, 114, 114, 114, 342, 137, 137, 137, 137, 137] 411 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 869 number of broken/clashed sets: 187 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054752 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054752 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054752/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054752 Building REAL250005054753 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054753' /scratch/stefan/7922901/working/building/REAL250005054753 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054753 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054753/0 /scratch/stefan/7922901/working/building/REAL250005054753 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/906 `/scratch/stefan/7922901/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005054753.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054753 none CC1=NC=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)O1 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', '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, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 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 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, 99, 59, 99, 37, 59, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 59, 59, 59, 37, 37, 26, 26, 7, 1] 119 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: 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: REAL250005054753 none CC1=NC=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)O1 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', '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, 1, 11, 8, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 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 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, 10, 10, 22, 22, 47, 67, 115, 115, 115, 119, 119, 119, 119, 119, 1, 2, 2, 2, 1, 22, 22, 22, 47, 47, 67, 67, 115, 119] 119 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: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054753 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054753 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054753/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054753 Building REAL250005054754 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054754' /scratch/stefan/7922901/working/building/REAL250005054754 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054754 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054754/0 /scratch/stefan/7922901/working/building/REAL250005054754 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/907 `/scratch/stefan/7922901/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054754.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054754 none COC(C)(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 127, 107, 127, 127, 77, 107, 38, 77, 24, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 133, 133, 133, 127, 127, 127, 127, 127, 127, 77, 77, 77, 38, 38, 24, 24, 7, 1] 133 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: 519 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054754 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054754 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054754/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054754 Building REAL250005054755 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054755' /scratch/stefan/7922901/working/building/REAL250005054755 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054755 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054755/0 /scratch/stefan/7922901/working/building/REAL250005054755 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/908 `/scratch/stefan/7922901/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC#N)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054755.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054755 none CC(CC#N)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [98, 73, 98, 125, 125, 56, 73, 37, 56, 25, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 125, 125, 56, 56, 56, 37, 37, 25, 25, 6, 1] 125 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: 576 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054755 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054755 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054755/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054755 Building REAL250005054756 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054756' /scratch/stefan/7922901/working/building/REAL250005054756 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054756 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054756/0 /scratch/stefan/7922901/working/building/REAL250005054756 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/909 `/scratch/stefan/7922901/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054756.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054756 none CCC1CC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 173, 112, 72, 112, 38, 72, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 173, 173, 173, 173, 72, 72, 72, 38, 38, 22, 22, 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: 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: REAL250005054756 none CCC1CC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 21, 21, 57, 83, 155, 155, 155, 173, 173, 173, 173, 173, 3, 3, 3, 3, 3, 1, 1, 1, 1, 21, 21, 21, 57, 57, 83, 83, 155, 173] 201 rigid atoms, others: [1, 2, 3, 4, 5, 25, 26, 27, 28] set([0, 6, 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, 36, 37]) total number of confs: 605 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054756 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054756 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054756/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054756 Building REAL250005054757 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054757' /scratch/stefan/7922901/working/building/REAL250005054757 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054757 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054757/0 /scratch/stefan/7922901/working/building/REAL250005054757 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/910 `/scratch/stefan/7922901/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)C(C)(C)O) `REAL250005054757.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054757 none C[C@@H](C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 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, 7, 7] 1 hydrogens need rotated 240 conformations in input total number of sets (complete confs): 240 using faster count positions algorithm for large data unique positions, atoms: [64, 62, 64, 49, 62, 30, 49, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 64, 80, 80, 80, 64, 64, 64, 49, 49, 49, 30, 30, 20, 20, 4, 1, 80, 80, 80, 80, 80, 80, 240] 240 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: 571 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054757 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054757 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054757/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054757 Building REAL250005054758 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054758' /scratch/stefan/7922901/working/building/REAL250005054758 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054758 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054758/0 /scratch/stefan/7922901/working/building/REAL250005054758 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/911 `/scratch/stefan/7922901/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1COC(=O)O1) `REAL250005054758.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054758 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1COC(=O)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 5, 3, 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: [20, 7, 20, 47, 72, 127, 127, 127, 134, 134, 134, 134, 134, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 47, 47, 72, 72, 127, 134, 1, 1, 1] 134 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 494 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: REAL250005054758 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1COC(=O)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 5, 3, 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: [71, 38, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 71, 123, 123, 134, 134, 134, 134, 134, 71, 71, 71, 38, 38, 25, 25, 8, 1, 134, 134, 134] 134 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 455 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054758 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054758 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054758/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054758 Building REAL250005054759 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054759' /scratch/stefan/7922901/working/building/REAL250005054759 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054759 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054759/0 /scratch/stefan/7922901/working/building/REAL250005054759 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/912 `/scratch/stefan/7922901/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C12CC(C1)OC2) `REAL250005054759.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054759 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C12CC(C1)OC2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 24, 47, 107, 107, 107, 110, 110, 110, 110, 110, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 47, 47, 107, 110, 1, 1, 1, 1, 1, 1, 1] 110 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 397 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054759 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C12CC(C1)OC2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [61, 34, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 61, 109, 109, 110, 110, 110, 110, 110, 61, 61, 61, 34, 34, 21, 21, 6, 1, 110, 110, 110, 110, 110, 110, 110] 110 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 381 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054759 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054759 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054759/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054759 Building REAL250005054760 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054760' /scratch/stefan/7922901/working/building/REAL250005054760 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054760 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054760/0 /scratch/stefan/7922901/working/building/REAL250005054760 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/913 `/scratch/stefan/7922901/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C1CC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054760.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054760 none CC(O)C1CC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 65, 49, 65, 30, 49, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 216, 72, 72, 72, 72, 49, 49, 49, 30, 30, 17, 17, 5, 1] 216 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: 479 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: REAL250005054760 none CC(O)C1CC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 6, 6, 12, 12, 26, 38, 72, 72, 72, 72, 72, 72, 72, 72, 2, 2, 2, 2, 6, 1, 1, 1, 1, 12, 12, 12, 26, 26, 38, 38, 72, 72] 216 rigid atoms, others: [1, 3, 4, 5, 6, 26, 27, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 279 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054760 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054760 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054760/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054760 Building REAL250005054761 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054761' /scratch/stefan/7922901/working/building/REAL250005054761 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054761 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054761/0 /scratch/stefan/7922901/working/building/REAL250005054761 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/914 `/scratch/stefan/7922901/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@]2(C(=O)N(C)CCNC(=O)C3=CC(=O)[N-]O3)C[C@@H]12) `REAL250005054761.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054761 none C[C@@H]1C[C@@]2(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 83, 55, 83, 28, 55, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 85, 56, 56, 56, 29, 29, 15, 15, 5, 1, 85, 85] 85 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054761 none C[C@@H]1C[C@@]2(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 8, 8, 26, 43, 83, 83, 83, 85, 85, 85, 85, 85, 1, 1, 1, 2, 2, 2, 1, 1, 8, 8, 8, 26, 26, 43, 43, 83, 85, 1, 1] 85 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 20, 21, 22, 26, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054761 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054761 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054761/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054761 Building REAL250005054762 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054762' /scratch/stefan/7922901/working/building/REAL250005054762 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054762 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054762/0 /scratch/stefan/7922901/working/building/REAL250005054762 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/915 `/scratch/stefan/7922901/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=NC=N1) `REAL250005054762.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054762 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=NC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 46, 97, 127, 201, 201, 201, 201, 201, 201, 201, 201, 8, 25, 1, 1, 1, 1, 1, 1, 46, 46, 46, 97, 97, 127, 127, 201, 201, 8, 8, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 786 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054762 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=NC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 53, 110, 110, 171, 201, 201, 201, 201, 53, 53, 53, 25, 25, 14, 14, 4, 1, 171, 171, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 714 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054762 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054762 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054762/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054762 Building REAL250005054763 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054763' /scratch/stefan/7922901/working/building/REAL250005054763 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054763 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054763/0 /scratch/stefan/7922901/working/building/REAL250005054763 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/916 `/scratch/stefan/7922901/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C[NH+](C)C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054763.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054763 none CC(C[NH+](C)C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 3, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 2, 1] 4 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: 19 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054763 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054763 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054763/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054763 Building REAL250005054764 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054764' /scratch/stefan/7922901/working/building/REAL250005054764 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054764 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054764/0 /scratch/stefan/7922901/working/building/REAL250005054764 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/917 `/scratch/stefan/7922901/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054764.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054764 none C=CC(C)(O)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 414 conformations in input total number of sets (complete confs): 414 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 118, 138, 138, 82, 118, 43, 82, 28, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 138, 138, 414, 82, 82, 82, 43, 43, 28, 28, 7, 1] 414 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: 952 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054764 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054764 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054764/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054764 Building REAL250005054765 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054765' /scratch/stefan/7922901/working/building/REAL250005054765 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054765 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054765/0 /scratch/stefan/7922901/working/building/REAL250005054765 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/918 `/scratch/stefan/7922901/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CO)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054765.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054765 none CCC(C)(CO)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 216 conformations in input total number of sets (complete confs): 216 using faster count positions algorithm for large data unique positions, atoms: [69, 53, 42, 53, 53, 67, 36, 42, 22, 36, 16, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 53, 53, 53, 67, 67, 201, 36, 36, 36, 22, 22, 16, 16, 5, 1] 216 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: 605 number of broken/clashed sets: 216 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054765 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054765 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054765/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054765 Building REAL250005054766 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054766' /scratch/stefan/7922901/working/building/REAL250005054766 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054766 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054766/0 /scratch/stefan/7922901/working/building/REAL250005054766 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/919 `/scratch/stefan/7922901/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1([NH+](C)C)CC1) `REAL250005054766.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054766 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1([NH+](C)C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 4, 5, 5, 6, 6, 6, 9, 9, 9, 9, 9, 1, 3, 1, 1, 4, 4, 4, 1, 1, 4, 4, 4, 5, 5, 5, 5, 6, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 9 rigid atoms, others: [37, 38, 39, 40, 13, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 39 number of broken/clashed sets: 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: REAL250005054766 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1([NH+](C)C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 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: 31 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054766 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054766/1 /scratch/stefan/7922901/working/building/REAL250005054766 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/920 `/scratch/stefan/7922901/working/3D/920' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054766.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054766 none CN(C)C1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 95, 69, 95, 38, 69, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 114, 114, 114, 69, 69, 69, 38, 38, 24, 24, 7, 1, 114, 114, 114, 114] 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, 36, 37, 38, 39]) total number of confs: 417 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: REAL250005054766 none CN(C)C1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 10, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 5, 5, 13, 13, 37, 60, 110, 110, 110, 114, 114, 114, 114, 114, 1, 1, 5, 5, 5, 5, 5, 5, 13, 13, 13, 37, 37, 60, 60, 110, 114, 1, 1, 1, 1] 114 rigid atoms, others: [1, 3, 4, 37, 38, 39, 19, 20, 36] set([0, 2, 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, 35]) total number of confs: 427 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054766 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054766 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054766/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054766/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054766 Building REAL250005054767 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054767' /scratch/stefan/7922901/working/building/REAL250005054767 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054767 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054767/0 /scratch/stefan/7922901/working/building/REAL250005054767 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/921 `/scratch/stefan/7922901/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054767.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054767 none CCCC=CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 125, 125, 53, 37, 53, 29, 37, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 177, 177, 125, 125, 37, 37, 37, 29, 29, 18, 18, 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: 846 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054767 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054767 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054767/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054767 Building REAL250005054768 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054768' /scratch/stefan/7922901/working/building/REAL250005054768 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054768 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054768/0 /scratch/stefan/7922901/working/building/REAL250005054768 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/922 `/scratch/stefan/7922901/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054768.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054768 none CC=C(F)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 120, 136, 75, 120, 45, 75, 30, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 75, 75, 75, 45, 45, 30, 30, 9, 1] 136 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: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054768 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054768 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054768/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054768 Building REAL250005054769 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054769' /scratch/stefan/7922901/working/building/REAL250005054769 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054769 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054769/0 /scratch/stefan/7922901/working/building/REAL250005054769 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/923 `/scratch/stefan/7922901/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005054769.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054769 none CCC(C(=O)N(C)CCNC(=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', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [79, 80, 63, 47, 63, 29, 47, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 80, 86, 86, 82, 82, 82, 82, 82, 80, 47, 47, 47, 29, 29, 20, 20, 4, 1, 86, 86, 86, 86, 86, 86, 86] 86 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: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054769 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054769 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054769/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054769 Building REAL250005054770 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054770' /scratch/stefan/7922901/working/building/REAL250005054770 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054770 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054770/0 /scratch/stefan/7922901/working/building/REAL250005054770 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/924 `/scratch/stefan/7922901/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005054770.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054770 none C[C@H](C(=O)N(C)CCNC(=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', '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, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 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 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 14, 13, 13, 12, 13, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 12, 12, 12, 12, 6, 1, 14, 14, 14, 14, 14, 14] 14 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: 53 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054770 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054770/1 /scratch/stefan/7922901/working/building/REAL250005054770 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/925 `/scratch/stefan/7922901/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)N(C)C) `REAL250005054770.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005054770 none C[C@H](C(=O)N(C)CCNC(=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', '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', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [101, 88, 101, 62, 88, 34, 62, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 101, 104, 104, 101, 101, 101, 62, 62, 62, 34, 34, 21, 21, 7, 1, 104, 104, 104, 104, 104, 104] 104 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: 389 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054770 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054770 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054770/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054770/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054770 Building REAL250005054771 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054771' /scratch/stefan/7922901/working/building/REAL250005054771 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054771 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054771/0 /scratch/stefan/7922901/working/building/REAL250005054771 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/926 `/scratch/stefan/7922901/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(CO)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054771.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054771 none CC(C)C(CO)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [95, 75, 95, 56, 75, 107, 43, 56, 25, 43, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95, 75, 107, 107, 321, 43, 43, 43, 25, 25, 16, 16, 4, 1] 330 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: 909 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054771 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054771 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054771/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054771 Building REAL250005054772 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054772' /scratch/stefan/7922901/working/building/REAL250005054772 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054772 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054772/0 /scratch/stefan/7922901/working/building/REAL250005054772 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/927 `/scratch/stefan/7922901/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054772.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054772 none CCOC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 131, 131, 57, 45, 57, 30, 45, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 131, 131, 45, 45, 45, 30, 30, 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: 601 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054772 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054772 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054772/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054772 Building REAL250005054773 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054773' /scratch/stefan/7922901/working/building/REAL250005054773 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005054773 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054773/0 /scratch/stefan/7922901/working/building/REAL250005054773 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/928 `/scratch/stefan/7922901/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+]1CCC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054773.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054773 none CC[N@@H+]1CCC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 23, 23, 23, 23, 23, 21, 20, 21, 17, 20, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 23, 23, 23, 23, 23, 20, 20, 20, 17, 17, 15, 15, 6, 1] 24 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: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054773 none CC[N@@H+]1CCC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 12, 13, 17, 17, 17, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 12, 12, 13, 13, 17, 23] 24 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 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, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054773 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054773/1 /scratch/stefan/7922901/working/building/REAL250005054773 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/929 `/scratch/stefan/7922901/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+]1CCC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054773.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054773 none CC[N@H+]1CCC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 22, 22, 22, 22, 22, 20, 19, 20, 16, 19, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 22, 22, 22, 22, 22, 19, 19, 19, 16, 16, 14, 14, 6, 1] 25 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: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054773 none CC[N@H+]1CCC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 12, 13, 17, 17, 17, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 12, 12, 13, 13, 17, 22] 25 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 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, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054773 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `2' /scratch/stefan/7922901/working/building/REAL250005054773/2 /scratch/stefan/7922901/working/building/REAL250005054773 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 2 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/930 `/scratch/stefan/7922901/working/3D/930' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054773.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005054773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054773/2/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: REAL250005054773 none CCN1CCC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 99, 99, 99, 99, 77, 56, 77, 31, 56, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 99, 99, 99, 99, 99, 56, 56, 56, 31, 31, 19, 19, 8, 1] 107 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: 405 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: REAL250005054773 none CCN1CCC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 47, 64, 93, 93, 93, 99, 99, 99, 99, 99, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 18, 18, 18, 47, 47, 64, 64, 93, 99] 107 rigid atoms, others: [1, 2, 3, 4, 5, 6, 26, 27, 28, 29, 30] set([0, 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, 38, 39]) total number of confs: 383 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054773 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054773 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054773/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054773/1.* 2: /scratch/stefan/7922901/working/building/REAL250005054773/2.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054773 Building REAL250005054774 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054774' /scratch/stefan/7922901/working/building/REAL250005054774 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054774 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054774/0 /scratch/stefan/7922901/working/building/REAL250005054774 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/931 `/scratch/stefan/7922901/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=C(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054774.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054774 none CCC(C)=C(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', '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, 5, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [191, 114, 114, 114, 86, 114, 64, 86, 34, 64, 22, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 191, 191, 191, 191, 191, 114, 114, 114, 114, 114, 114, 64, 64, 64, 34, 34, 22, 22, 7, 1] 191 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: 883 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054774 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054774 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054774/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054774 Building REAL250005054775 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054775' /scratch/stefan/7922901/working/building/REAL250005054775 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054775 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054775/0 /scratch/stefan/7922901/working/building/REAL250005054775 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/932 `/scratch/stefan/7922901/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005054775.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054775 none COC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 100, 72, 100, 35, 72, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 134, 134, 72, 72, 72, 35, 35, 22, 22, 7, 1, 134, 134, 134, 134, 134, 134] 134 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: 476 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054775 none COC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 1, 1, 5, 5, 13, 13, 41, 64, 126, 126, 126, 134, 134, 134, 134, 134, 1, 1, 1, 5, 5, 5, 13, 13, 13, 41, 41, 64, 64, 126, 134, 1, 1, 1, 1, 1, 1] 134 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: 472 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054775 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054775 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054775/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054775 Building REAL250005054776 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054776' /scratch/stefan/7922901/working/building/REAL250005054776 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054776 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054776/0 /scratch/stefan/7922901/working/building/REAL250005054776 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/933 `/scratch/stefan/7922901/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054776.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054776 none C=CCCC(=O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 183, 65, 41, 65, 39, 41, 27, 39, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 183, 183, 39, 39, 39, 27, 27, 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: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054776 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054776 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054776/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054776 Building REAL250005054777 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054777' /scratch/stefan/7922901/working/building/REAL250005054777 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054777 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054777/0 /scratch/stefan/7922901/working/building/REAL250005054777 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/934 `/scratch/stefan/7922901/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054777.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054777 none CC(O)CCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 138, 201, 99, 85, 39, 39, 39, 31, 39, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 134, 137, 108, 108, 86, 86, 39, 39, 39, 31, 31, 20, 20, 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: 1650 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054777 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054777 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054777/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054777 Building REAL250005054778 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054778' /scratch/stefan/7922901/working/building/REAL250005054778 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054778 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054778/0 /scratch/stefan/7922901/working/building/REAL250005054778 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/935 `/scratch/stefan/7922901/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)OCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054778.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054778 none CC(=O)OCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 103, 70, 59, 70, 43, 59, 23, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 126, 126, 126, 103, 103, 59, 59, 59, 43, 43, 23, 23, 6, 1] 126 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: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054778 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054778 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054778/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054778 Building REAL250005054779 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054779' /scratch/stefan/7922901/working/building/REAL250005054779 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054779 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054779/0 /scratch/stefan/7922901/working/building/REAL250005054779 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/936 `/scratch/stefan/7922901/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054779.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054779 none CC(=O)NCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 121, 83, 61, 47, 61, 31, 47, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 121, 121, 83, 83, 47, 47, 47, 31, 31, 20, 20, 4, 1] 157 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: 672 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054779 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054779 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054779/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054779 Building REAL250005054780 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054780' /scratch/stefan/7922901/working/building/REAL250005054780 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054780 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054780/0 /scratch/stefan/7922901/working/building/REAL250005054780 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/937 `/scratch/stefan/7922901/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNC(=O)N1) `REAL250005054780.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054780 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 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: [32, 11, 32, 75, 102, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 32, 32, 32, 75, 75, 102, 102, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 727 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: REAL250005054780 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 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: [69, 33, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 69, 134, 134, 201, 201, 201, 201, 201, 69, 69, 69, 33, 33, 22, 22, 4, 1, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 566 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054780 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054780 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054780/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054780 Building REAL250005054781 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054781' /scratch/stefan/7922901/working/building/REAL250005054781 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054781 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054781/0 /scratch/stefan/7922901/working/building/REAL250005054781 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/938 `/scratch/stefan/7922901/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)[NH+](C)C) `REAL250005054781.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054781 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)[NH+](C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 7 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 23 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054781 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054781 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054781/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054781 Building REAL250005054782 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054782' /scratch/stefan/7922901/working/building/REAL250005054782 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054782 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054782/0 /scratch/stefan/7922901/working/building/REAL250005054782 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/939 `/scratch/stefan/7922901/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)(F)CO) `REAL250005054782.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054782 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)(F)CO NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 15, 15, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 573 conformations in input total number of sets (complete confs): 573 using faster count positions algorithm for large data unique positions, atoms: [114, 52, 31, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 114, 186, 186, 187, 187, 187, 191, 114, 114, 114, 52, 52, 31, 31, 9, 1, 191, 191, 573] 573 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 1229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054782 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054782 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054782/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054782 Building REAL250005054783 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054783' /scratch/stefan/7922901/working/building/REAL250005054783 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054783 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054783/0 /scratch/stefan/7922901/working/building/REAL250005054783 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/940 `/scratch/stefan/7922901/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C#CC1(C)CC1) `REAL250005054783.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054783 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C#CC1(C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 31, 61, 142, 142, 142, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 31, 31, 61, 61, 142, 148, 2, 2, 2, 1, 1, 1, 1] 148 rigid atoms, others: [1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 531 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054783 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C#CC1(C)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [79, 45, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 79, 148, 148, 148, 148, 148, 148, 148, 79, 79, 79, 45, 45, 25, 25, 7, 1, 148, 148, 148, 148, 148, 148, 148] 148 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 508 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054783 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054783 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054783/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054783 Building REAL250005054784 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054784' /scratch/stefan/7922901/working/building/REAL250005054784 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054784 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054784/0 /scratch/stefan/7922901/working/building/REAL250005054784 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/941 `/scratch/stefan/7922901/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054784.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054784 none CC(=O)C=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 65, 67, 65, 53, 45, 53, 27, 45, 20, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 67, 67, 67, 65, 65, 45, 45, 45, 27, 27, 20, 20, 7, 1] 67 rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 246 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054784 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054784 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054784/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054784 Building REAL250005054785 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054785' /scratch/stefan/7922901/working/building/REAL250005054785 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054785 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054785/0 /scratch/stefan/7922901/working/building/REAL250005054785 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/942 `/scratch/stefan/7922901/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)COC1CC1) `REAL250005054785.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054785 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)COC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 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: [86, 58, 86, 136, 161, 201, 201, 201, 201, 201, 201, 201, 201, 26, 58, 6, 1, 1, 1, 1, 85, 86, 86, 136, 136, 161, 161, 201, 201, 26, 26, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL250005054785 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)COC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 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: [59, 29, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 59, 89, 89, 110, 150, 201, 201, 59, 59, 59, 29, 29, 16, 16, 4, 1, 110, 110, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054785 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054785 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054785/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054785 Building REAL250005054786 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054786' /scratch/stefan/7922901/working/building/REAL250005054786 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054786 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054786/0 /scratch/stefan/7922901/working/building/REAL250005054786 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/943 `/scratch/stefan/7922901/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC=CN1) `REAL250005054786.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054786 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC=CN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 4, 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: [17, 6, 17, 45, 65, 142, 142, 142, 144, 144, 144, 144, 144, 1, 6, 1, 1, 1, 1, 1, 17, 17, 17, 45, 45, 65, 65, 142, 144, 1, 1, 1] 144 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 511 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054786 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC=CN1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 4, 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: [48, 30, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 48, 68, 68, 68, 68, 68, 68, 48, 48, 48, 30, 30, 23, 23, 9, 1, 68, 68, 68] 68 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054786 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054786 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054786/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054786 Building REAL250005054787 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054787' /scratch/stefan/7922901/working/building/REAL250005054787 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054787 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054787/0 /scratch/stefan/7922901/working/building/REAL250005054787 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/944 `/scratch/stefan/7922901/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CC1CCC1) `REAL250005054787.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054787 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CC1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 77, 145, 163, 201, 201, 201, 201, 201, 201, 201, 201, 8, 42, 8, 1, 1, 1, 1, 1, 77, 77, 77, 145, 145, 163, 163, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 770 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: REAL250005054787 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CC1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 98, 98, 158, 158, 201, 201, 201, 65, 65, 65, 41, 41, 19, 19, 4, 1, 158, 158, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 740 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054787 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054787 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054787/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054787 Building REAL250005054788 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054788' /scratch/stefan/7922901/working/building/REAL250005054788 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054788 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054788/0 /scratch/stefan/7922901/working/building/REAL250005054788 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/945 `/scratch/stefan/7922901/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN=CS1) `REAL250005054788.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054788 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN=CS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 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: [29, 10, 29, 75, 113, 197, 197, 197, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 29, 29, 29, 75, 75, 113, 113, 197, 201, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 742 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054788 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NN=CS1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 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: [109, 52, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 109, 186, 186, 201, 201, 201, 201, 109, 109, 109, 52, 52, 30, 30, 7, 1, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29]) total number of confs: 669 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054788 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054788 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054788/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054788 Building REAL250005054789 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054789' /scratch/stefan/7922901/working/building/REAL250005054789 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054789 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054789/0 /scratch/stefan/7922901/working/building/REAL250005054789 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/946 `/scratch/stefan/7922901/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC(=O)CO1) `REAL250005054789.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054789 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC(=O)CO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 17, 43, 64, 128, 128, 128, 133, 133, 133, 133, 133, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 43, 43, 64, 64, 128, 133, 1, 1, 1, 1, 1] 133 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 479 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: REAL250005054789 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC(=O)CO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [77, 38, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 77, 124, 124, 133, 133, 133, 133, 133, 77, 77, 77, 38, 38, 23, 23, 7, 1, 133, 133, 133, 133, 133] 133 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 455 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054789 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054789 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054789/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054789 Building REAL250005054790 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054790' /scratch/stefan/7922901/working/building/REAL250005054790 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054790 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054790/0 /scratch/stefan/7922901/working/building/REAL250005054790 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/947 `/scratch/stefan/7922901/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054790.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054790 none CC(C)NC(=O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 201, 199, 145, 199, 83, 145, 40, 83, 22, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 199, 83, 83, 83, 40, 40, 22, 22, 6, 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: 685 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054790 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054790 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054790/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054790 Building REAL250005054791 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054791' /scratch/stefan/7922901/working/building/REAL250005054791 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054791 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054791/0 /scratch/stefan/7922901/working/building/REAL250005054791 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/948 `/scratch/stefan/7922901/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005054791.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054791 none CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 88, 70, 88, 39, 70, 26, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 118, 118, 70, 70, 70, 39, 39, 26, 26, 7, 1, 118, 118, 118, 118] 118 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: 380 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: REAL250005054791 none CC1=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 17, 17, 43, 63, 112, 114, 112, 118, 118, 118, 118, 118, 1, 1, 1, 2, 2, 2, 17, 17, 17, 43, 43, 63, 63, 114, 118, 1, 1, 1, 1] 118 rigid atoms, others: [0, 1, 2, 3, 36, 35, 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: 433 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054791 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054791 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054791/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054791 Building REAL250005054792 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054792' /scratch/stefan/7922901/working/building/REAL250005054792 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054792 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054792/0 /scratch/stefan/7922901/working/building/REAL250005054792 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/949 `/scratch/stefan/7922901/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC=CN1C) `REAL250005054792.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054792 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC=CN1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 8, 23, 56, 86, 169, 169, 169, 173, 173, 173, 173, 173, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 56, 56, 86, 86, 169, 173, 1, 1, 2, 2, 2] 173 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 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, 32, 33, 34]) total number of confs: 646 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054792 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NC=CN1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [90, 44, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 90, 165, 165, 173, 173, 173, 173, 173, 90, 90, 90, 44, 44, 30, 30, 7, 1, 173, 173, 173, 173, 173] 173 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054792 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054792 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054792/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054792 Building REAL250005054793 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054793' /scratch/stefan/7922901/working/building/REAL250005054793 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054793 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054793/0 /scratch/stefan/7922901/working/building/REAL250005054793 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/950 `/scratch/stefan/7922901/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054793.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054793 none CC(CO)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 423 conformations in input total number of sets (complete confs): 423 using faster count positions algorithm for large data unique positions, atoms: [140, 107, 140, 141, 76, 107, 46, 76, 30, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 141, 141, 423, 76, 76, 76, 46, 46, 30, 30, 9, 1] 423 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: 1011 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054793 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054793 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054793/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054793 Building REAL250005054794 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054794' /scratch/stefan/7922901/working/building/REAL250005054794 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054794 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054794/0 /scratch/stefan/7922901/working/building/REAL250005054794 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/951 `/scratch/stefan/7922901/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CON=C1) `REAL250005054794.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054794 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CON=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [23, 11, 23, 62, 93, 201, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 23, 23, 23, 62, 62, 93, 93, 201, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 746 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: REAL250005054794 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CON=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [65, 31, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 65, 115, 115, 201, 201, 201, 201, 65, 65, 65, 31, 31, 20, 20, 6, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 548 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054794 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054794 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054794/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054794 Building REAL250005054795 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054795' /scratch/stefan/7922901/working/building/REAL250005054795 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054795 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054795/0 /scratch/stefan/7922901/working/building/REAL250005054795 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/952 `/scratch/stefan/7922901/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCCO) `REAL250005054795.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054795 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCCO NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [78, 37, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 78, 120, 120, 132, 157, 201, 201, 78, 78, 78, 37, 37, 22, 22, 4, 1, 132, 132, 157, 157, 201, 201, 201, 201, 603] 603 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1447 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054795 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054795 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054795/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054795 Building REAL250005054796 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054796' /scratch/stefan/7922901/working/building/REAL250005054796 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054796 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054796/0 /scratch/stefan/7922901/working/building/REAL250005054796 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/953 `/scratch/stefan/7922901/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(=O)C1CC1) `REAL250005054796.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054796 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [75, 37, 75, 138, 160, 201, 201, 201, 201, 201, 201, 201, 201, 12, 37, 1, 12, 1, 1, 1, 75, 75, 75, 138, 138, 160, 160, 201, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 15, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 808 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: REAL250005054796 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 39, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 72, 120, 120, 150, 151, 201, 201, 72, 72, 72, 39, 39, 24, 24, 4, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 704 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054796 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054796 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054796/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054796 Building REAL250005054797 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054797' /scratch/stefan/7922901/working/building/REAL250005054797 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054797 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054797/0 /scratch/stefan/7922901/working/building/REAL250005054797 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/954 `/scratch/stefan/7922901/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1COC(=O)N1) `REAL250005054797.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054797 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1COC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 6, 4, 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: [24, 6, 24, 71, 103, 178, 178, 178, 184, 184, 184, 184, 184, 1, 6, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 71, 71, 103, 103, 178, 184, 1, 1, 1] 184 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 704 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: REAL250005054797 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1COC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 6, 4, 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: [94, 46, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 94, 158, 158, 184, 184, 184, 184, 184, 184, 94, 94, 94, 46, 46, 28, 28, 9, 1, 184, 184, 184] 184 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 643 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054797 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054797 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054797/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054797 Building REAL250005054798 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054798' /scratch/stefan/7922901/working/building/REAL250005054798 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054798 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054798/0 /scratch/stefan/7922901/working/building/REAL250005054798 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/955 `/scratch/stefan/7922901/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1(O)CC1) `REAL250005054798.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054798 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1(O)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [50, 23, 50, 115, 147, 201, 201, 201, 201, 201, 201, 201, 201, 8, 23, 1, 1, 1, 1, 1, 50, 50, 50, 115, 115, 147, 147, 201, 201, 8, 8, 6, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 810 number of broken/clashed sets: 188 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054798 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1(O)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [64, 34, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 64, 125, 125, 180, 201, 201, 201, 64, 64, 64, 34, 34, 18, 18, 4, 1, 181, 181, 603, 201, 201, 201, 201] 603 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1394 number of broken/clashed sets: 188 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054798 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054798 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054798/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054798 Building REAL250005054799 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054799' /scratch/stefan/7922901/working/building/REAL250005054799 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054799 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054799/0 /scratch/stefan/7922901/working/building/REAL250005054799 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/956 `/scratch/stefan/7922901/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC1F) `REAL250005054799.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054799 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC1F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 6, 19, 50, 68, 108, 108, 108, 113, 113, 113, 113, 113, 1, 6, 1, 1, 1, 1, 1, 19, 19, 19, 50, 50, 68, 68, 108, 113, 1, 1, 1, 1, 1, 1] 113 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 416 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: REAL250005054799 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC1F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [65, 36, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 64, 101, 101, 113, 113, 113, 113, 65, 65, 65, 36, 36, 23, 23, 8, 1, 113, 113, 113, 113, 113, 113] 113 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 410 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054799 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054799 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054799/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054799 Building REAL250005054800 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054800' /scratch/stefan/7922901/working/building/REAL250005054800 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054800 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054800/0 /scratch/stefan/7922901/working/building/REAL250005054800 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/957 `/scratch/stefan/7922901/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)C1CCC1) `REAL250005054800.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054800 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)C1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 11, 18, 56, 84, 195, 195, 195, 195, 195, 195, 195, 195, 5, 11, 1, 5, 1, 1, 1, 1, 18, 18, 18, 56, 56, 84, 84, 195, 195, 5, 1, 1, 1, 1, 1, 1, 1] 195 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 705 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: REAL250005054800 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)C1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [69, 30, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 69, 126, 126, 127, 127, 195, 195, 195, 69, 69, 69, 30, 30, 16, 16, 4, 1, 127, 195, 195, 195, 195, 195, 195, 195] 195 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 701 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054800 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054800 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054800/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054800 Building REAL250005054801 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054801' /scratch/stefan/7922901/working/building/REAL250005054801 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054801 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054801/0 /scratch/stefan/7922901/working/building/REAL250005054801 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/958 `/scratch/stefan/7922901/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC(C)(C)O1) `REAL250005054801.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054801 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC(C)(C)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 15, 38, 61, 121, 121, 121, 128, 128, 128, 128, 128, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 38, 38, 61, 61, 121, 128, 1, 1, 1, 2, 2, 2, 2, 2, 2] 128 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 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, 33, 34, 35, 36, 37, 38]) total number of confs: 468 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054801 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC(C)(C)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [68, 40, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 68, 116, 116, 128, 128, 128, 128, 128, 68, 68, 68, 40, 40, 26, 26, 8, 1, 128, 128, 128, 128, 128, 128, 128, 128, 128] 128 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054801 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054801 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054801/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054801 Building REAL250005054802 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054802' /scratch/stefan/7922901/working/building/REAL250005054802 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054802 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054802/0 /scratch/stefan/7922901/working/building/REAL250005054802 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/959 `/scratch/stefan/7922901/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1CF) `REAL250005054802.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054802 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 21, 54, 83, 167, 167, 167, 182, 182, 182, 182, 182, 1, 8, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 54, 54, 83, 83, 167, 182, 1, 1, 9, 9] 201 rigid atoms, others: [32, 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, 33, 34]) total number of confs: 651 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: REAL250005054802 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1CF NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 37, 20, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 77, 128, 129, 182, 182, 182, 182, 182, 201, 78, 78, 78, 37, 37, 20, 20, 4, 1, 182, 182, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 770 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054802 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054802 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054802/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054802 Building REAL250005054803 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054803' /scratch/stefan/7922901/working/building/REAL250005054803 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054803 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054803/0 /scratch/stefan/7922901/working/building/REAL250005054803 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/960 `/scratch/stefan/7922901/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)=C1CCC1) `REAL250005054803.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054803 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)=C1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'F', 'C.2', '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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 10, 30, 81, 114, 201, 201, 201, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 81, 81, 114, 114, 201, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 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]) 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: REAL250005054803 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)=C1CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'F', 'C.2', '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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 37, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 78, 172, 172, 201, 201, 201, 201, 201, 78, 78, 78, 37, 37, 20, 20, 5, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 652 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054803 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054803 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054803/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054803 Building REAL250005054804 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054804' /scratch/stefan/7922901/working/building/REAL250005054804 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054804 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054804/0 /scratch/stefan/7922901/working/building/REAL250005054804 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/961 `/scratch/stefan/7922901/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054804.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054804 none CCC(CO)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 354 conformations in input total number of sets (complete confs): 354 using faster count positions algorithm for large data unique positions, atoms: [98, 85, 57, 85, 115, 46, 57, 23, 46, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 85, 115, 115, 345, 46, 46, 46, 23, 23, 12, 12, 4, 1] 354 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: 1022 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054804 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054804 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054804/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054804 Building REAL250005054805 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054805' /scratch/stefan/7922901/working/building/REAL250005054805 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054805 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054805/0 /scratch/stefan/7922901/working/building/REAL250005054805 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/962 `/scratch/stefan/7922901/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(O)C1CC1) `REAL250005054805.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054805 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(O)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [34, 22, 34, 74, 83, 123, 123, 123, 123, 123, 123, 123, 123, 11, 22, 5, 1, 5, 1, 1, 1, 34, 34, 34, 74, 74, 83, 83, 123, 123, 11, 11, 5, 15, 1, 1, 1, 1, 1] 369 rigid atoms, others: [34, 35, 36, 37, 38, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 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: REAL250005054805 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(O)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 369 conformations in input total number of sets (complete confs): 369 using faster count positions algorithm for large data unique positions, atoms: [40, 18, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 40, 56, 56, 57, 86, 86, 123, 123, 40, 40, 40, 18, 18, 9, 9, 3, 1, 57, 57, 86, 258, 123, 123, 123, 123, 123] 369 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054805 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054805 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054805/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054805 Building REAL250005054806 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054806' /scratch/stefan/7922901/working/building/REAL250005054806 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054806 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054806/0 /scratch/stefan/7922901/working/building/REAL250005054806 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/963 `/scratch/stefan/7922901/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1CC1)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054806.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054806 none CC(=CC1CC1)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 78, 127, 127, 201, 201, 52, 78, 28, 52, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 201, 201, 201, 201, 201, 52, 52, 52, 28, 28, 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: 763 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: REAL250005054806 none CC(=CC1CC1)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 5, 19, 19, 47, 47, 101, 130, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 47, 47, 47, 101, 101, 130, 130, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 25, 26, 27, 28, 29] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 766 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054806 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054806 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054806/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054806 Building REAL250005054807 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054807' /scratch/stefan/7922901/working/building/REAL250005054807 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054807 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054807/0 /scratch/stefan/7922901/working/building/REAL250005054807 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/964 `/scratch/stefan/7922901/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@@H]1C#N) `REAL250005054807.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054807 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@@H]1C#N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 12, 28, 41, 61, 61, 61, 64, 64, 64, 64, 64, 1, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 28, 28, 41, 41, 61, 64, 1, 1] 64 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 248 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: REAL250005054807 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@@H]1C#N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [44, 28, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 43, 59, 59, 64, 64, 64, 64, 64, 64, 44, 44, 44, 28, 28, 18, 18, 5, 1, 64, 64] 64 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 235 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054807 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054807 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054807/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054807 Building REAL250005054808 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054808' /scratch/stefan/7922901/working/building/REAL250005054808 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054808 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054808/0 /scratch/stefan/7922901/working/building/REAL250005054808 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/965 `/scratch/stefan/7922901/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CN=CO1) `REAL250005054808.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054808 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CN=CO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 23, 51, 107, 143, 201, 201, 201, 201, 201, 201, 201, 201, 5, 23, 1, 1, 1, 1, 1, 1, 51, 51, 51, 107, 107, 143, 143, 201, 201, 5, 5, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 804 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054808 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1=CN=CO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 1, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 28, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 51, 89, 89, 151, 201, 201, 201, 201, 51, 51, 51, 28, 28, 16, 16, 4, 1, 151, 151, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 687 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054808 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054808 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054808/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054808 Building REAL250005054809 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054809' /scratch/stefan/7922901/working/building/REAL250005054809 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054809 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054809/0 /scratch/stefan/7922901/working/building/REAL250005054809 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/966 `/scratch/stefan/7922901/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COCC1) `REAL250005054809.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054809 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 19, 68, 106, 197, 199, 199, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 19, 19, 19, 68, 68, 106, 106, 199, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 773 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: REAL250005054809 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=COCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 43, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 84, 156, 156, 201, 201, 201, 201, 84, 84, 84, 43, 43, 28, 28, 8, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 614 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054809 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054809 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054809/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054809 Building REAL250005054810 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054810' /scratch/stefan/7922901/working/building/REAL250005054810 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054810 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054810/0 /scratch/stefan/7922901/working/building/REAL250005054810 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/967 `/scratch/stefan/7922901/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC(C)(C)O) `REAL250005054810.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054810 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCC(C)(C)O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 309 conformations in input total number of sets (complete confs): 309 using faster count positions algorithm for large data unique positions, atoms: [37, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 37, 57, 57, 61, 61, 103, 103, 103, 37, 37, 37, 23, 23, 14, 14, 4, 1, 61, 61, 61, 61, 103, 103, 103, 103, 103, 103, 309] 309 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 795 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054810 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054810 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054810/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054810 Building REAL250005054811 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054811' /scratch/stefan/7922901/working/building/REAL250005054811 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054811 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054811/0 /scratch/stefan/7922901/working/building/REAL250005054811 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/968 `/scratch/stefan/7922901/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005054811.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054811 none CC1=CC=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 143, 79, 143, 42, 79, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 79, 79, 79, 42, 42, 26, 26, 8, 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: 587 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: REAL250005054811 none CC1=CC=C(C(=O)N(C)CCNC(=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', '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, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 11, 11, 27, 27, 73, 105, 197, 197, 197, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 27, 27, 27, 73, 73, 105, 105, 197, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 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: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054811 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054811 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054811/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054811 Building REAL250005054812 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054812' /scratch/stefan/7922901/working/building/REAL250005054812 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054812 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054812/0 /scratch/stefan/7922901/working/building/REAL250005054812 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/969 `/scratch/stefan/7922901/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(O)CC1) `REAL250005054812.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054812 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 375 conformations in input total number of sets (complete confs): 375 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 15, 48, 66, 122, 122, 122, 125, 125, 125, 125, 125, 1, 7, 1, 1, 1, 1, 15, 15, 15, 48, 48, 66, 66, 122, 125, 6, 1, 1, 1, 1] 375 rigid atoms, others: [32, 13, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 466 number of broken/clashed sets: 102 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054812 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(O)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 375 conformations in input total number of sets (complete confs): 375 using faster count positions algorithm for large data unique positions, atoms: [75, 41, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 75, 106, 106, 125, 125, 125, 75, 75, 75, 41, 41, 26, 26, 5, 1, 375, 125, 125, 125, 125] 375 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 828 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054812 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054812 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054812/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054812 Building REAL250005054813 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054813' /scratch/stefan/7922901/working/building/REAL250005054813 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054813 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054813/0 /scratch/stefan/7922901/working/building/REAL250005054813 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/970 `/scratch/stefan/7922901/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCC1) `REAL250005054813.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054813 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 11, 25, 57, 75, 138, 138, 138, 148, 148, 148, 148, 148, 1, 11, 1, 1, 1, 1, 25, 25, 25, 57, 57, 75, 75, 138, 148, 1, 1, 1, 1, 1] 148 rigid atoms, others: [32, 13, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 509 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: REAL250005054813 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [101, 61, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 101, 148, 148, 148, 148, 148, 101, 101, 101, 61, 61, 36, 36, 11, 1, 148, 148, 148, 148, 148] 148 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 535 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054813 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054813 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054813/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054813 Building REAL250005054814 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054814' /scratch/stefan/7922901/working/building/REAL250005054814 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054814 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054814/0 /scratch/stefan/7922901/working/building/REAL250005054814 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/971 `/scratch/stefan/7922901/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)=NO1) `REAL250005054814.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054814 none CC1CC(C(=O)N(C)CCNC(=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', '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, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 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, 138, 85, 138, 52, 85, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 172, 172, 172, 172, 85, 85, 85, 52, 52, 33, 33, 9, 1] 172 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: 543 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054814 none CC1CC(C(=O)N(C)CCNC(=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', '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, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 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, 1, 1, 9, 9, 31, 31, 76, 97, 167, 167, 167, 172, 172, 172, 172, 172, 1, 1, 2, 2, 2, 1, 1, 1, 31, 31, 31, 76, 76, 97, 97, 167, 172] 172 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054814 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054814 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054814/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054814 Building REAL250005054815 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054815' /scratch/stefan/7922901/working/building/REAL250005054815 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054815 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054815/0 /scratch/stefan/7922901/working/building/REAL250005054815 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/972 `/scratch/stefan/7922901/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054815.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054815 none CC(CF)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [126, 94, 126, 131, 67, 94, 41, 67, 26, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 131, 131, 67, 67, 67, 41, 41, 26, 26, 7, 1] 131 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: 563 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054815 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054815 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054815/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054815 Building REAL250005054816 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054816' /scratch/stefan/7922901/working/building/REAL250005054816 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054816 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054816/0 /scratch/stefan/7922901/working/building/REAL250005054816 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/973 `/scratch/stefan/7922901/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(Cl)=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054816.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054816 none CC(Cl)=CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 16, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 79, 57, 77, 35, 59, 24, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 59, 59, 59, 35, 35, 24, 24, 9, 1] 110 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: 398 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054816 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054816 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054816/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054816 Building REAL250005054817 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054817' /scratch/stefan/7922901/working/building/REAL250005054817 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054817 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054817/0 /scratch/stefan/7922901/working/building/REAL250005054817 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/974 `/scratch/stefan/7922901/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054817.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054817 none CC=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 75, 51, 75, 33, 51, 22, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 51, 51, 51, 33, 33, 22, 22, 8, 1] 85 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: 322 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054817 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054817 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054817/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054817 Building REAL250005054818 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054818' /scratch/stefan/7922901/working/building/REAL250005054818 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054818 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054818/0 /scratch/stefan/7922901/working/building/REAL250005054818 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/975 `/scratch/stefan/7922901/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)(F)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054818.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054818 none CCC(F)(F)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [100, 100, 77, 101, 101, 63, 77, 32, 63, 24, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 63, 63, 63, 32, 32, 24, 24, 7, 1] 103 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: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054818 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054818 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054818/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054818 Building REAL250005054819 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054819' /scratch/stefan/7922901/working/building/REAL250005054819 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054819 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054819/0 /scratch/stefan/7922901/working/building/REAL250005054819 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/976 `/scratch/stefan/7922901/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CC1F) `REAL250005054819.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054819 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CC1F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 8, 22, 36, 80, 80, 80, 83, 83, 83, 83, 83, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 36, 36, 80, 83, 2, 2, 2, 1, 1, 1] 83 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 300 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: REAL250005054819 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CC1F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [54, 30, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 54, 82, 82, 83, 83, 83, 83, 54, 54, 54, 30, 30, 21, 21, 7, 1, 83, 83, 83, 83, 83, 83] 83 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 294 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054819 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054819 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054819/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054819 Building REAL250005054820 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054820' /scratch/stefan/7922901/working/building/REAL250005054820 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054820 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054820/0 /scratch/stefan/7922901/working/building/REAL250005054820 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/977 `/scratch/stefan/7922901/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCC(=O)O1) `REAL250005054820.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054820 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCC(=O)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 5, 3, 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: [21, 7, 21, 50, 76, 130, 130, 130, 144, 144, 144, 144, 144, 1, 7, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 50, 50, 76, 76, 130, 144, 1, 1, 1, 1] 144 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 529 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: REAL250005054820 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCC(=O)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 5, 3, 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: [76, 37, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 75, 130, 131, 144, 144, 144, 144, 144, 144, 76, 76, 76, 37, 37, 25, 25, 9, 1, 144, 144, 144, 144] 144 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 485 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054820 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054820 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054820/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054820 Building REAL250005054821 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054821' /scratch/stefan/7922901/working/building/REAL250005054821 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054821 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054821/0 /scratch/stefan/7922901/working/building/REAL250005054821 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/978 `/scratch/stefan/7922901/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CCF) `REAL250005054821.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054821 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=CCF NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [93, 56, 32, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 91, 111, 113, 149, 149, 157, 93, 93, 93, 56, 56, 32, 32, 11, 1, 149, 149, 157, 157] 157 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 599 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054821 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054821 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054821/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054821 Building REAL250005054822 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054822' /scratch/stefan/7922901/working/building/REAL250005054822 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054822 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054822/0 /scratch/stefan/7922901/working/building/REAL250005054822 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/979 `/scratch/stefan/7922901/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)CC1CC1) `REAL250005054822.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054822 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)CC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 41, 96, 131, 201, 201, 201, 201, 201, 201, 201, 201, 12, 25, 3, 12, 1, 1, 1, 1, 41, 41, 41, 96, 96, 131, 131, 201, 201, 12, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 802 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: REAL250005054822 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)CC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 66, 102, 102, 103, 103, 151, 201, 201, 66, 66, 66, 35, 35, 20, 20, 4, 1, 103, 151, 151, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 805 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054822 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054822 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054822/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054822 Building REAL250005054823 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054823' /scratch/stefan/7922901/working/building/REAL250005054823 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054823 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054823/0 /scratch/stefan/7922901/working/building/REAL250005054823 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/980 `/scratch/stefan/7922901/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1COC(=O)N1) `REAL250005054823.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054823 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1COC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 6, 4, 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: [24, 6, 24, 70, 102, 177, 177, 177, 183, 183, 183, 183, 183, 1, 6, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 70, 70, 102, 102, 177, 183, 1, 1, 1] 183 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 701 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: REAL250005054823 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1COC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 12, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 3, 7, 6, 4, 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: [94, 46, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 94, 157, 157, 183, 183, 183, 183, 183, 183, 94, 94, 94, 46, 46, 28, 28, 9, 1, 183, 183, 183] 183 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 635 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054823 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054823 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054823/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054823 Building REAL250005054824 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054824' /scratch/stefan/7922901/working/building/REAL250005054824 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054824 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054824/0 /scratch/stefan/7922901/working/building/REAL250005054824 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/981 `/scratch/stefan/7922901/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCCC#N) `REAL250005054824.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054824 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCCC#N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 49, 81, 81, 87, 111, 137, 201, 201, 49, 49, 49, 25, 25, 16, 16, 4, 1, 87, 87, 111, 111, 137, 137, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 914 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054824 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054824 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054824/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054824 Building REAL250005054825 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054825' /scratch/stefan/7922901/working/building/REAL250005054825 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054825 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054825/0 /scratch/stefan/7922901/working/building/REAL250005054825 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/982 `/scratch/stefan/7922901/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CO)CC1) `REAL250005054825.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054825 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CO)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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 435 conformations in input total number of sets (complete confs): 435 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 9, 27, 46, 121, 121, 121, 139, 139, 139, 139, 139, 1, 3, 1, 1, 10, 1, 1, 9, 9, 9, 27, 27, 46, 46, 121, 139, 10, 10, 30, 1, 1, 1, 1] 435 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 504 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054825 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CO)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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 435 conformations in input total number of sets (complete confs): 435 using faster count positions algorithm for large data unique positions, atoms: [81, 41, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 80, 125, 125, 139, 145, 139, 139, 81, 81, 81, 41, 41, 23, 23, 8, 1, 145, 145, 435, 139, 139, 139, 139] 435 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 969 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054825 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054825 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054825/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054825 Building REAL250005054826 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054826' /scratch/stefan/7922901/working/building/REAL250005054826 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054826 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054826/0 /scratch/stefan/7922901/working/building/REAL250005054826 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/983 `/scratch/stefan/7922901/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NO1) `REAL250005054826.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054826 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 12, 28, 84, 117, 199, 199, 199, 201, 201, 201, 201, 201, 1, 12, 1, 1, 1, 1, 1, 28, 28, 28, 84, 84, 117, 117, 199, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005054826 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=NO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 54, 32, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 98, 179, 179, 201, 201, 201, 201, 98, 98, 98, 54, 54, 32, 32, 8, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 643 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054826 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054826 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054826/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054826 Building REAL250005054827 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054827' /scratch/stefan/7922901/working/building/REAL250005054827 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005054827 as failed and skipping /scratch/stefan/7922901/working /scratch/stefan/7922901 `/scratch/stefan/7922901/working/building/REAL250005054827' -> `/scratch/stefan/7922901/failed/REAL250005054827' Building REAL250005054828 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054828' /scratch/stefan/7922901/working/building/REAL250005054828 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054828 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054828/0 /scratch/stefan/7922901/working/building/REAL250005054828 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/984 `/scratch/stefan/7922901/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC(=O)N1) `REAL250005054828.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054828 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 6, 4, 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: [25, 7, 25, 72, 106, 189, 189, 189, 193, 193, 193, 193, 193, 1, 7, 1, 1, 1, 1, 1, 1, 25, 25, 25, 72, 72, 106, 106, 189, 193, 1, 1, 1, 1, 1, 1] 193 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 750 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054828 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CCC(=O)N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 6, 4, 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: [94, 46, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 94, 168, 168, 193, 193, 193, 193, 193, 94, 94, 94, 46, 46, 28, 28, 8, 1, 193, 193, 193, 193, 193, 193] 193 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 657 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054828 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054828 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054828/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054828 Building REAL250005054829 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054829' /scratch/stefan/7922901/working/building/REAL250005054829 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054829 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054829/0 /scratch/stefan/7922901/working/building/REAL250005054829 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/985 `/scratch/stefan/7922901/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054829.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054829 none C[C@H](O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [53, 49, 53, 53, 42, 49, 25, 42, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 53, 53, 53, 159, 42, 42, 42, 25, 25, 17, 17, 7, 1] 159 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: 368 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054829 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054829 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054829/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054829 Building REAL250005054830 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054830' /scratch/stefan/7922901/working/building/REAL250005054830 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054830 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054830/0 /scratch/stefan/7922901/working/building/REAL250005054830 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/986 `/scratch/stefan/7922901/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=C(F)O1) `REAL250005054830.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054830 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=C(F)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 15, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 12, 30, 76, 112, 199, 199, 199, 201, 201, 201, 201, 201, 1, 12, 1, 1, 1, 1, 1, 1, 30, 30, 30, 76, 76, 112, 112, 199, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 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]) 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: REAL250005054830 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC=C(F)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 1, 1, 15, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 48, 27, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 96, 173, 173, 201, 201, 201, 201, 201, 96, 96, 96, 48, 48, 27, 27, 6, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054830 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054830 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054830/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054830 Building REAL250005054831 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054831' /scratch/stefan/7922901/working/building/REAL250005054831 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054831 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054831/0 /scratch/stefan/7922901/working/building/REAL250005054831 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/987 `/scratch/stefan/7922901/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054831.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054831 none CON=CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.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, 8, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 98, 67, 98, 49, 67, 30, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 67, 67, 67, 49, 49, 30, 30, 9, 1] 130 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: 492 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054831 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054831 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054831/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054831 Building REAL250005054832 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054832' /scratch/stefan/7922901/working/building/REAL250005054832 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054832 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054832/0 /scratch/stefan/7922901/working/building/REAL250005054832 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/988 `/scratch/stefan/7922901/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054832.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054832 none C#CCC(C)(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 55, 55, 55, 55, 41, 55, 27, 41, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 65, 65, 55, 55, 55, 55, 55, 55, 41, 41, 41, 27, 27, 16, 16, 4, 1] 65 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: 286 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054832 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054832 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054832/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054832 Building REAL250005054833 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054833' /scratch/stefan/7922901/working/building/REAL250005054833 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054833 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054833/0 /scratch/stefan/7922901/working/building/REAL250005054833 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/989 `/scratch/stefan/7922901/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC(C)(F)C1) `REAL250005054833.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054833 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC(C)(F)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 76, 112, 199, 199, 199, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 29, 29, 29, 76, 76, 112, 112, 199, 201, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 36, 37, 13, 15, 16, 17, 18, 19, 20, 30, 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, 33, 34, 35]) total number of confs: 772 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: REAL250005054833 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC(C)(F)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 68, 147, 147, 201, 201, 201, 201, 201, 70, 70, 70, 36, 36, 20, 20, 5, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 713 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054833 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054833 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054833/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054833 Building REAL250005054834 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054834' /scratch/stefan/7922901/working/building/REAL250005054834 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054834 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054834/0 /scratch/stefan/7922901/working/building/REAL250005054834 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/990 `/scratch/stefan/7922901/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(OC)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054834.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054834 none CCC(C)(OC)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 59, 51, 59, 59, 71, 44, 51, 22, 44, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 59, 59, 59, 71, 71, 71, 44, 44, 44, 22, 22, 12, 12, 4, 1] 81 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: 377 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054834 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054834 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054834/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054834 Building REAL250005054835 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054835' /scratch/stefan/7922901/working/building/REAL250005054835 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054835 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054835/0 /scratch/stefan/7922901/working/building/REAL250005054835 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/991 `/scratch/stefan/7922901/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054835.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054835 none CC(C)[C@H](O)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 390 conformations in input total number of sets (complete confs): 390 using faster count positions algorithm for large data unique positions, atoms: [130, 114, 130, 83, 114, 114, 62, 83, 34, 62, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 342, 62, 62, 62, 34, 34, 23, 23, 7, 1] 390 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: 903 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054835 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054835 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054835/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054835 Building REAL250005054836 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054836' /scratch/stefan/7922901/working/building/REAL250005054836 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054836 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054836/0 /scratch/stefan/7922901/working/building/REAL250005054836 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/992 `/scratch/stefan/7922901/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054836.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054836 none C#CC1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 105, 77, 105, 40, 77, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 143, 143, 143, 77, 77, 77, 40, 40, 24, 24, 7, 1, 143, 143, 143, 143] 143 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: 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: REAL250005054836 none C#CC1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 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, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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, 3, 3, 11, 11, 41, 67, 135, 135, 135, 143, 143, 143, 143, 143, 1, 1, 1, 11, 11, 11, 41, 41, 67, 67, 135, 143, 1, 1, 1, 1] 143 rigid atoms, others: [0, 1, 2, 3, 33, 32, 18, 19, 20, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054836 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054836 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054836/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054836 Building REAL250005054837 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054837' /scratch/stefan/7922901/working/building/REAL250005054837 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054837 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054837/0 /scratch/stefan/7922901/working/building/REAL250005054837 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/993 `/scratch/stefan/7922901/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCC(=O)O1) `REAL250005054837.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054837 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCC(=O)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 7, 25, 67, 103, 192, 192, 192, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 67, 67, 103, 103, 192, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 747 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: REAL250005054837 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1CCC(=O)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 47, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 86, 173, 173, 201, 201, 201, 201, 201, 201, 86, 86, 86, 47, 47, 29, 29, 9, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 674 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054837 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054837 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054837/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054837 Building REAL250005054838 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054838' /scratch/stefan/7922901/working/building/REAL250005054838 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054838 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054838/0 /scratch/stefan/7922901/working/building/REAL250005054838 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/994 `/scratch/stefan/7922901/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC=CCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054838.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054838 none C=CC=CCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 138, 63, 59, 63, 41, 59, 26, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 138, 138, 59, 59, 59, 41, 41, 26, 26, 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: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054838 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054838 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054838/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054838 Building REAL250005054839 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054839' /scratch/stefan/7922901/working/building/REAL250005054839 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054839 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054839/0 /scratch/stefan/7922901/working/building/REAL250005054839 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/995 `/scratch/stefan/7922901/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005054839.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054839 none C#CC1(C(=O)N(C)CCNC(=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', '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: [1, 1, 5, 1, 11, 8, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 115, 91, 115, 46, 91, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 91, 91, 91, 46, 46, 30, 30, 9, 1, 158, 158, 158, 158, 158, 158] 158 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054839 none C#CC1(C(=O)N(C)CCNC(=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', '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: [1, 1, 5, 1, 11, 8, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 11, 11, 39, 71, 148, 148, 148, 158, 158, 158, 158, 158, 1, 1, 1, 1, 11, 11, 11, 39, 39, 71, 71, 148, 158, 1, 1, 1, 1, 1, 1] 158 rigid atoms, others: [0, 1, 2, 3, 36, 33, 35, 32, 34, 18, 19, 20, 21, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 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/7922901/working/building/REAL250005054839 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054839 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054839/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054839 Building REAL250005054840 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054840' /scratch/stefan/7922901/working/building/REAL250005054840 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005054840 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054840/0 /scratch/stefan/7922901/working/building/REAL250005054840 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/996 `/scratch/stefan/7922901/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCC[N@@H+]1C) `REAL250005054840.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054840 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCC[N@@H+]1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 7, 7, 9, 9, 9, 12, 12, 12, 12, 12, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 9, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2] 12 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 46 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: REAL250005054840 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCC[N@@H+]1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 8, 8, 5, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054840 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054840/1 /scratch/stefan/7922901/working/building/REAL250005054840 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/997 `/scratch/stefan/7922901/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCC[N@H+]1C) `REAL250005054840.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054840 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCC[N@H+]1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2] 7 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 23 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: REAL250005054840 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CCC[N@H+]1C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.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'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] 7 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 29 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054840 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054840 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054840/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054840/1.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054840 Building REAL250005054841 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054841' /scratch/stefan/7922901/working/building/REAL250005054841 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054841 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054841/0 /scratch/stefan/7922901/working/building/REAL250005054841 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/998 `/scratch/stefan/7922901/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC=CCO1) `REAL250005054841.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054841 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC=CCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 41, 59, 106, 106, 106, 114, 114, 114, 114, 114, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 16, 41, 41, 59, 59, 106, 114, 1, 1, 1, 1, 1, 1, 1] 114 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 397 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: REAL250005054841 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1CC=CCO1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [71, 36, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 108, 108, 114, 114, 114, 114, 114, 71, 71, 71, 36, 36, 25, 25, 9, 1, 114, 114, 114, 114, 114, 114, 114] 114 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 388 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054841 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054841 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054841/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054841 Building REAL250005054842 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054842' /scratch/stefan/7922901/working/building/REAL250005054842 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054842 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054842/0 /scratch/stefan/7922901/working/building/REAL250005054842 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/999 `/scratch/stefan/7922901/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC(C)(C)C1) `REAL250005054842.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054842 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC(C)(C)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 11, 29, 71, 100, 188, 188, 188, 194, 194, 194, 194, 194, 1, 11, 1, 1, 1, 1, 1, 1, 29, 29, 29, 71, 71, 100, 100, 188, 194, 1, 2, 2, 2, 2, 2, 2, 1, 1] 194 rigid atoms, others: [37, 38, 13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 709 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: REAL250005054842 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CC(C)(C)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [98, 47, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 98, 189, 189, 194, 194, 194, 194, 194, 98, 98, 98, 47, 47, 33, 33, 9, 1, 194, 194, 194, 194, 194, 194, 194, 194, 194] 194 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 626 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054842 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054842 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054842/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054842 Building REAL250005054843 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054843' /scratch/stefan/7922901/working/building/REAL250005054843 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054843 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054843/0 /scratch/stefan/7922901/working/building/REAL250005054843 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1000 `/scratch/stefan/7922901/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#C[C@H]1C[C@H]1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054843.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054843 none C#C[C@H]1C[C@H]1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 58, 63, 43, 58, 26, 43, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 63, 63, 63, 43, 43, 43, 26, 26, 17, 17, 7, 1] 63 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: 227 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: REAL250005054843 none C#C[C@H]1C[C@H]1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 25, 33, 59, 59, 59, 63, 63, 63, 63, 63, 1, 1, 1, 13, 13, 13, 25, 25, 33, 33, 59, 63] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054843 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054843 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054843/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054843 Building REAL250005054844 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054844' /scratch/stefan/7922901/working/building/REAL250005054844 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054844 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054844/0 /scratch/stefan/7922901/working/building/REAL250005054844 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1001 `/scratch/stefan/7922901/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(N=[N+]=[N-])CC1) `REAL250005054844.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054844 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(N=[N+]=[N-])CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 58, 82, 163, 163, 163, 171, 171, 171, 171, 171, 1, 6, 1, 1, 13, 13, 1, 1, 17, 17, 17, 58, 58, 82, 82, 163, 171, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 15, 16, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 619 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: REAL250005054844 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(N=[N+]=[N-])CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'N.2', 'N.1', 'N.1', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 42, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 85, 144, 144, 171, 201, 201, 171, 171, 86, 86, 86, 42, 42, 24, 24, 4, 1, 171, 171, 171, 171] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 658 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054844 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054844 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054844/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054844 Building REAL250005054845 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054845' /scratch/stefan/7922901/working/building/REAL250005054845 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054845 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054845/0 /scratch/stefan/7922901/working/building/REAL250005054845 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1002 `/scratch/stefan/7922901/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)OC) `REAL250005054845.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054845 none CCC(CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 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, 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, 98, 73, 48, 40, 48, 27, 40, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 98, 100, 101, 101, 101, 101, 101, 98, 73, 73, 40, 40, 40, 27, 27, 17, 17, 4, 1, 100, 100, 100] 101 rigid atoms, others: [37, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 465 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054845 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054845 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054845/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054845 Building REAL250005054846 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054846' /scratch/stefan/7922901/working/building/REAL250005054846 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054846 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054846/0 /scratch/stefan/7922901/working/building/REAL250005054846 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1003 `/scratch/stefan/7922901/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CSC=N1) `REAL250005054846.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054846 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CSC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 10, 23, 61, 95, 187, 187, 187, 201, 201, 201, 201, 201, 1, 10, 1, 1, 1, 1, 1, 23, 23, 23, 61, 61, 95, 95, 187, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 691 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054846 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CSC=N1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 52, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 107, 192, 192, 201, 201, 201, 201, 107, 107, 107, 52, 52, 34, 34, 11, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 675 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054846 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054846 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054846/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054846 Building REAL250005054847 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054847' /scratch/stefan/7922901/working/building/REAL250005054847 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054847 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054847/0 /scratch/stefan/7922901/working/building/REAL250005054847 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1004 `/scratch/stefan/7922901/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054847.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054847 none CC=C(CC)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [185, 185, 140, 185, 195, 77, 140, 44, 77, 27, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 185, 185, 185, 185, 195, 195, 195, 195, 195, 77, 77, 77, 44, 44, 27, 27, 7, 1] 195 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: 727 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054847 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054847 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054847/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054847 Building REAL250005054848 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054848' /scratch/stefan/7922901/working/building/REAL250005054848 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054848 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054848/0 /scratch/stefan/7922901/working/building/REAL250005054848 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1005 `/scratch/stefan/7922901/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC12CC(C1)C2) `REAL250005054848.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054848 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC12CC(C1)C2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 15, 35, 48, 98, 98, 98, 98, 98, 98, 98, 98, 6, 9, 1, 1, 1, 1, 1, 1, 16, 16, 16, 35, 35, 48, 48, 98, 98, 6, 6, 1, 1, 1, 1, 1, 1, 1] 98 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 359 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: REAL250005054848 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC12CC(C1)C2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [51, 27, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 51, 94, 94, 98, 98, 98, 98, 98, 51, 51, 51, 27, 27, 16, 16, 4, 1, 98, 98, 98, 98, 98, 98, 98, 98, 98] 98 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 346 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054848 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054848 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054848/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054848 Building REAL250005054849 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054849' /scratch/stefan/7922901/working/building/REAL250005054849 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054849 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054849/0 /scratch/stefan/7922901/working/building/REAL250005054849 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1006 `/scratch/stefan/7922901/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1)C(C)O) `REAL250005054849.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054849 none CCC(C(=O)N(C)CCNC(=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', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [58, 56, 46, 40, 46, 26, 40, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 56, 70, 70, 59, 59, 59, 59, 59, 56, 40, 40, 40, 26, 26, 18, 18, 4, 1, 70, 70, 70, 70, 210] 210 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: 551 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054849 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054849 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054849/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054849 Building REAL250005054850 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054850' /scratch/stefan/7922901/working/building/REAL250005054850 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054850 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054850/0 /scratch/stefan/7922901/working/building/REAL250005054850 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1007 `/scratch/stefan/7922901/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054850.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054850 none COC(F)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 110, 189, 83, 110, 38, 83, 23, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 189, 83, 83, 83, 38, 38, 23, 23, 8, 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: 794 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054850 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054850 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054850/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054850 Building REAL250005054851 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054851' /scratch/stefan/7922901/working/building/REAL250005054851 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054851 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054851/0 /scratch/stefan/7922901/working/building/REAL250005054851 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1008 `/scratch/stefan/7922901/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C#N)CCC1) `REAL250005054851.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054851 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C#N)CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', '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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 8, 27, 47, 94, 94, 94, 98, 98, 98, 98, 98, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 27, 27, 47, 47, 94, 98, 1, 1, 1, 1, 1, 1] 98 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 30, 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]) 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: REAL250005054851 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C#N)CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', '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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [54, 31, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 54, 92, 92, 98, 98, 98, 98, 98, 54, 54, 54, 31, 31, 20, 20, 7, 1, 98, 98, 98, 98, 98, 98] 98 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054851 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054851 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054851/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054851 Building REAL250005054852 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054852' /scratch/stefan/7922901/working/building/REAL250005054852 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054852 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054852/0 /scratch/stefan/7922901/working/building/REAL250005054852 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1009 `/scratch/stefan/7922901/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=C1CCCC1) `REAL250005054852.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054852 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=C1CCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 9, 36, 96, 132, 199, 199, 199, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 36, 36, 36, 96, 96, 132, 132, 199, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 803 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: REAL250005054852 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C=C1CCCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 76, 142, 142, 201, 201, 201, 201, 201, 76, 76, 76, 40, 40, 22, 22, 6, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 695 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054852 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054852 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054852/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054852 Building REAL250005054853 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054853' /scratch/stefan/7922901/working/building/REAL250005054853 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054853 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054853/0 /scratch/stefan/7922901/working/building/REAL250005054853 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1010 `/scratch/stefan/7922901/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(C)(C)C#N) `REAL250005054853.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054853 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC(C)(C)C#N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 66, 116, 116, 142, 201, 201, 201, 201, 68, 68, 68, 34, 34, 20, 20, 4, 1, 142, 142, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 860 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054853 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054853 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054853/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054853 Building REAL250005054854 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054854' /scratch/stefan/7922901/working/building/REAL250005054854 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054854 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054854/0 /scratch/stefan/7922901/working/building/REAL250005054854 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1011 `/scratch/stefan/7922901/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054854.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054854 none COCC(O)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 339 conformations in input total number of sets (complete confs): 339 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 99, 71, 99, 55, 71, 32, 55, 22, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 99, 297, 55, 55, 55, 32, 32, 22, 22, 5, 1] 339 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054854 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054854 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054854/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054854 Building REAL250005054855 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054855' /scratch/stefan/7922901/working/building/REAL250005054855 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054855 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054855/0 /scratch/stefan/7922901/working/building/REAL250005054855 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1012 `/scratch/stefan/7922901/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CC1(F)F) `REAL250005054855.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054855 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CC1(F)F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 8, 19, 55, 76, 127, 127, 127, 130, 130, 130, 130, 130, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 19, 55, 55, 76, 76, 127, 130, 1, 1] 130 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 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]) total number of confs: 479 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054855 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CC1(F)F NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [69, 41, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 69, 107, 107, 130, 130, 130, 130, 130, 69, 69, 69, 41, 41, 25, 25, 8, 1, 130, 130] 130 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 465 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054855 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054855 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054855/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054855 Building REAL250005054856 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054856' /scratch/stefan/7922901/working/building/REAL250005054856 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054856 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054856/0 /scratch/stefan/7922901/working/building/REAL250005054856 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1013 `/scratch/stefan/7922901/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1C#N) `REAL250005054856.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054856 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1C#N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 26, 71, 107, 200, 200, 200, 201, 201, 201, 201, 201, 1, 8, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 71, 71, 107, 107, 200, 201, 1, 1] 201 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 752 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: REAL250005054856 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1C[C@H]1C#N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 41, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 85, 151, 151, 201, 201, 201, 201, 201, 201, 86, 86, 86, 41, 41, 23, 23, 5, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 711 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054856 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054856 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054856/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054856 Building REAL250005054857 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054857' /scratch/stefan/7922901/working/building/REAL250005054857 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054857 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054857/0 /scratch/stefan/7922901/working/building/REAL250005054857 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1014 `/scratch/stefan/7922901/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054857.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054857 none C=C(C)CCCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 116, 92, 35, 33, 35, 25, 33, 16, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 192, 192, 131, 131, 93, 93, 33, 33, 33, 25, 25, 16, 16, 6, 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: 968 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054857 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054857 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054857/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054857 Building REAL250005054858 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054858' /scratch/stefan/7922901/working/building/REAL250005054858 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054858 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054858/0 /scratch/stefan/7922901/working/building/REAL250005054858 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1015 `/scratch/stefan/7922901/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1C[C@@H](O)C1) `REAL250005054858.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054858 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 564 conformations in input total number of sets (complete confs): 564 using faster count positions algorithm for large data unique positions, atoms: [26, 8, 26, 67, 95, 179, 179, 179, 188, 188, 188, 188, 188, 1, 8, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 67, 67, 95, 95, 179, 188, 1, 1, 6, 1, 1] 564 rigid atoms, others: [32, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 701 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: REAL250005054858 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H]1C[C@@H](O)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 564 conformations in input total number of sets (complete confs): 564 using faster count positions algorithm for large data unique positions, atoms: [78, 42, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 76, 143, 145, 188, 188, 188, 188, 188, 188, 78, 78, 78, 42, 42, 26, 26, 7, 1, 188, 188, 564, 188, 188] 564 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 1238 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054858 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054858 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054858/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054858 Building REAL250005054859 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054859' /scratch/stefan/7922901/working/building/REAL250005054859 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054859 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054859/0 /scratch/stefan/7922901/working/building/REAL250005054859 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1016 `/scratch/stefan/7922901/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CC1(C)C) `REAL250005054859.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054859 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CC1(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 46, 101, 120, 201, 201, 201, 201, 201, 201, 201, 201, 5, 25, 1, 1, 1, 1, 1, 1, 46, 46, 46, 101, 101, 120, 120, 201, 201, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 740 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: REAL250005054859 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CC1(C)C NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 26, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 60, 111, 111, 159, 201, 201, 201, 201, 60, 60, 60, 26, 26, 17, 17, 4, 1, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 785 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054859 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054859 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054859/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054859 Building REAL250005054860 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054860' /scratch/stefan/7922901/working/building/REAL250005054860 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054860 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054860/0 /scratch/stefan/7922901/working/building/REAL250005054860 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1017 `/scratch/stefan/7922901/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=C(Cl)CC1) `REAL250005054860.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054860 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=C(Cl)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 31, 85, 119, 200, 201, 201, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 31, 31, 31, 85, 85, 119, 119, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005054860 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=C(Cl)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 16, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 85, 152, 152, 201, 201, 201, 201, 85, 85, 85, 41, 41, 24, 24, 6, 1, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 601 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054860 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054860 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054860/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054860 Building REAL250005054861 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054861' /scratch/stefan/7922901/working/building/REAL250005054861 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054861 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054861/0 /scratch/stefan/7922901/working/building/REAL250005054861 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1018 `/scratch/stefan/7922901/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@]12C[C@H]1[C@H](F)C2) `REAL250005054861.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054861 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@]12C[C@H]1[C@H](F)C2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 9, 36, 63, 126, 126, 126, 135, 135, 135, 135, 135, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 36, 36, 63, 63, 126, 135, 1, 1, 1, 1] 135 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 493 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054861 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@]12C[C@H]1[C@H](F)C2 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 7, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [74, 38, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 73, 126, 126, 135, 135, 135, 135, 135, 135, 135, 74, 74, 74, 38, 38, 22, 22, 6, 1, 135, 135, 135, 135] 135 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054861 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054861 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054861/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054861 Building REAL250005054862 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054862' /scratch/stefan/7922901/working/building/REAL250005054862 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054862 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054862/0 /scratch/stefan/7922901/working/building/REAL250005054862 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1019 `/scratch/stefan/7922901/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNC(=O)O1) `REAL250005054862.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054862 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNC(=O)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 6, 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: [36, 12, 36, 79, 115, 198, 198, 198, 201, 201, 201, 201, 201, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 36, 79, 79, 115, 115, 198, 201, 1, 1] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30, 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]) 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: REAL250005054862 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=CNC(=O)O1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 1, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 6, 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, 52, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 99, 179, 179, 201, 201, 201, 201, 201, 99, 99, 99, 52, 52, 30, 30, 7, 1, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 643 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054862 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054862 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054862/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054862 Building REAL250005054863 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054863' /scratch/stefan/7922901/working/building/REAL250005054863 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054863 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054863/0 /scratch/stefan/7922901/working/building/REAL250005054863 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1020 `/scratch/stefan/7922901/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H]1C[C@H]1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054863.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054863 none CC(C)[C@@H]1C[C@H]1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 143, 143, 143, 95, 143, 61, 95, 33, 61, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 143, 143, 143, 143, 61, 61, 61, 33, 33, 20, 20, 8, 1] 143 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: 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: REAL250005054863 none CC(C)[C@@H]1C[C@H]1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 58, 80, 138, 138, 138, 143, 143, 143, 143, 143, 4, 4, 4, 4, 4, 4, 4, 1, 1, 23, 23, 23, 58, 58, 80, 80, 138, 143] 143 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 528 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054863 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054863 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054863/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054863 Building REAL250005054864 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054864' /scratch/stefan/7922901/working/building/REAL250005054864 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054864 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054864/0 /scratch/stefan/7922901/working/building/REAL250005054864 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1021 `/scratch/stefan/7922901/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)COCCO) `REAL250005054864.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054864 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)COCCO NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 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: [44, 23, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 44, 62, 62, 78, 141, 199, 201, 44, 44, 44, 23, 23, 12, 12, 4, 1, 78, 78, 199, 199, 201, 201, 603] 603 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1347 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054864 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054864 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054864/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054864 Building REAL250005054865 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054865' /scratch/stefan/7922901/working/building/REAL250005054865 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054865 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054865/0 /scratch/stefan/7922901/working/building/REAL250005054865 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1022 `/scratch/stefan/7922901/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)CF) `REAL250005054865.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054865 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)CF NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [49, 30, 20, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 49, 49, 49, 77, 77, 77, 77, 49, 49, 49, 30, 30, 20, 20, 6, 1, 77, 77, 77, 77, 77, 77, 77, 77] 77 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 351 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054865 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054865 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054865/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054865 Building REAL250005054866 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054866' /scratch/stefan/7922901/working/building/REAL250005054866 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054866 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054866/0 /scratch/stefan/7922901/working/building/REAL250005054866 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1023 `/scratch/stefan/7922901/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054866.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054866 none CC(C)[C@@H](O)CC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 7, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [186, 152, 186, 115, 152, 152, 78, 65, 78, 37, 65, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 186, 186, 456, 115, 115, 65, 65, 65, 37, 37, 22, 22, 4, 1] 558 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: 1328 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054866 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054866 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054866/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054866 Building REAL250005054867 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054867' /scratch/stefan/7922901/working/building/REAL250005054867 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054867 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054867/0 /scratch/stefan/7922901/working/building/REAL250005054867 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1024 `/scratch/stefan/7922901/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)CO) `REAL250005054867.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054867 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)CO NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 204 conformations in input total number of sets (complete confs): 204 using faster count positions algorithm for large data unique positions, atoms: [48, 28, 16, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 48, 48, 48, 68, 68, 68, 68, 48, 48, 48, 28, 28, 16, 16, 6, 1, 68, 68, 68, 68, 68, 68, 68, 68, 204] 204 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 511 number of broken/clashed sets: 204 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054867 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054867 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054867/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054867 Building REAL250005054868 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054868' /scratch/stefan/7922901/working/building/REAL250005054868 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054868 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054868/0 /scratch/stefan/7922901/working/building/REAL250005054868 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1025 `/scratch/stefan/7922901/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054868.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054868 none C=CCC(C)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 86, 146, 65, 86, 38, 65, 24, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 146, 146, 146, 146, 65, 65, 65, 38, 38, 24, 24, 6, 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: 912 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054868 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054868 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054868/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054868 Building REAL250005054869 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054869' /scratch/stefan/7922901/working/building/REAL250005054869 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054869 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054869/0 /scratch/stefan/7922901/working/building/REAL250005054869 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1026 `/scratch/stefan/7922901/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054869.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054869 none CC1CCCC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 32, 39, 22, 32, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 32, 32, 32, 22, 22, 16, 16, 6, 1] 39 rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 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: REAL250005054869 none CC1CCCC1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 10, 15, 37, 37, 37, 39, 39, 39, 39, 39, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 15, 15, 37, 39] 39 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: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054869 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054869 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054869/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054869 Building REAL250005054870 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054870' /scratch/stefan/7922901/working/building/REAL250005054870 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054870 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054870/0 /scratch/stefan/7922901/working/building/REAL250005054870 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1027 `/scratch/stefan/7922901/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CC[C@@H]2C[C@@H]21) `REAL250005054870.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054870 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CC[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [11, 3, 11, 32, 53, 111, 111, 111, 121, 121, 121, 121, 121, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 32, 32, 53, 53, 111, 121, 1, 1, 1, 1, 1, 1] 121 rigid atoms, others: [33, 34, 35, 36, 37, 38, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 429 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: REAL250005054870 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@@H]1CC[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [84, 45, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 83, 121, 121, 121, 121, 121, 121, 121, 121, 121, 121, 84, 84, 84, 45, 45, 28, 28, 9, 1, 121, 121, 121, 121, 121, 121] 121 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 438 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054870 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054870 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054870/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054870 Building REAL250005054871 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054871' /scratch/stefan/7922901/working/building/REAL250005054871 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054871 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054871/0 /scratch/stefan/7922901/working/building/REAL250005054871 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1028 `/scratch/stefan/7922901/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CC(F)C1) `REAL250005054871.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054871 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CC(F)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 23, 39, 86, 86, 86, 90, 90, 90, 90, 90, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 39, 39, 86, 90, 2, 2, 2, 1, 1, 1, 1, 1] 90 rigid atoms, others: [33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 332 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: REAL250005054871 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(C)CC(F)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 31, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 60, 90, 90, 90, 90, 90, 90, 90, 60, 60, 60, 31, 31, 22, 22, 8, 1, 90, 90, 90, 90, 90, 90, 90, 90] 90 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 310 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054871 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054871 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054871/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054871 Building REAL250005054872 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054872' /scratch/stefan/7922901/working/building/REAL250005054872 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054872 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054872/0 /scratch/stefan/7922901/working/building/REAL250005054872 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1029 `/scratch/stefan/7922901/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054872.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054872 none C[C@@H]1C[C@H]1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 87, 121, 55, 87, 32, 55, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 55, 55, 55, 32, 32, 20, 20, 6, 1] 121 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: 456 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: REAL250005054872 none C[C@@H]1C[C@H]1C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 18, 18, 41, 55, 117, 117, 117, 121, 121, 121, 121, 121, 2, 2, 2, 1, 1, 18, 18, 18, 41, 41, 55, 55, 117, 121] 121 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: 426 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054872 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054872 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054872/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054872 Building REAL250005054873 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054873' /scratch/stefan/7922901/working/building/REAL250005054873 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054873 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054873/0 /scratch/stefan/7922901/working/building/REAL250005054873 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1030 `/scratch/stefan/7922901/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)O) `REAL250005054873.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054873 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)O NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 486 conformations in input total number of sets (complete confs): 486 using faster count positions algorithm for large data unique positions, atoms: [90, 46, 28, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 90, 127, 127, 162, 162, 162, 90, 90, 90, 46, 46, 28, 28, 11, 1, 162, 162, 162, 162, 162, 162, 486] 486 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1141 number of broken/clashed sets: 346 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054873 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054873 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054873/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054873 Building REAL250005054874 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054874' /scratch/stefan/7922901/working/building/REAL250005054874 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054874 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054874/0 /scratch/stefan/7922901/working/building/REAL250005054874 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1031 `/scratch/stefan/7922901/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1(C(=O)N(C)CCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005054874.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054874 none CSC1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 150, 84, 150, 42, 84, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 199, 199, 201, 201, 201, 84, 84, 84, 42, 42, 24, 24, 4, 1, 199, 199, 199, 199] 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: 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: REAL250005054874 none CSC1(C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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, 14, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 16, 16, 56, 91, 199, 199, 199, 199, 199, 199, 199, 199, 1, 1, 8, 8, 8, 16, 16, 16, 56, 56, 91, 91, 199, 199, 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: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054874 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054874 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054874/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054874 Building REAL250005054875 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054875' /scratch/stefan/7922901/working/building/REAL250005054875 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054875 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054875/0 /scratch/stefan/7922901/working/building/REAL250005054875 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1032 `/scratch/stefan/7922901/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NOCC1) `REAL250005054875.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054875 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NOCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 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: [27, 9, 27, 76, 105, 169, 170, 169, 171, 171, 171, 171, 171, 1, 9, 1, 1, 1, 1, 1, 27, 27, 27, 76, 76, 105, 105, 170, 171, 1, 1, 1, 1] 171 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 662 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: REAL250005054875 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1=NOCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 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: [80, 40, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 80, 146, 146, 171, 171, 171, 171, 80, 80, 80, 40, 40, 25, 25, 9, 1, 171, 171, 171, 171] 171 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 531 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054875 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054875 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054875/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054875 Building REAL250005054876 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054876' /scratch/stefan/7922901/working/building/REAL250005054876 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054876 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054876/0 /scratch/stefan/7922901/working/building/REAL250005054876 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1033 `/scratch/stefan/7922901/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054876.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054876 none CC(C#N)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 136, 171, 171, 92, 63, 92, 36, 63, 24, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 171, 171, 171, 170, 137, 137, 63, 63, 63, 36, 36, 24, 24, 7, 1] 171 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: 734 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054876 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054876 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054876/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054876 Building REAL250005054877 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054877' /scratch/stefan/7922901/working/building/REAL250005054877 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005054877 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054877/0 /scratch/stefan/7922901/working/building/REAL250005054877 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1034 `/scratch/stefan/7922901/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C[N@H+](C)C1CC1) `REAL250005054877.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054877 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C[N@H+](C)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1] 4 rigid atoms, others: [36, 37, 38, 39, 40, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 19 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054877 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C[N@H+](C)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 2, 2, 2, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 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: 15 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054877 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `1' /scratch/stefan/7922901/working/building/REAL250005054877/1 /scratch/stefan/7922901/working/building/REAL250005054877 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 1 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1035 `/scratch/stefan/7922901/working/3D/1035' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C[N@@H+](C)C1CC1) `REAL250005054877.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005054877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054877 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C[N@@H+](C)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1] 4 rigid atoms, others: [36, 37, 38, 39, 40, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 19 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054877 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C[N@@H+](C)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 2, 2, 2, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 30] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 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: 22 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054877 /scratch/stefan/7922901/working /scratch/stefan/7922901 mkdir: created directory `2' /scratch/stefan/7922901/working/building/REAL250005054877/2 /scratch/stefan/7922901/working/building/REAL250005054877 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 2 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1036 `/scratch/stefan/7922901/working/3D/1036' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN(C)C1CC1) `REAL250005054877.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005054877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054877/2/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: REAL250005054877 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN(C)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 20, 40, 53, 80, 80, 80, 86, 86, 86, 86, 86, 7, 10, 3, 1, 3, 1, 1, 1, 20, 20, 20, 40, 40, 53, 53, 80, 86, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1] 86 rigid atoms, others: [35, 36, 37, 38, 39, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 339 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054877 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN(C)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [58, 33, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 58, 82, 82, 85, 86, 86, 86, 86, 58, 58, 58, 33, 33, 22, 22, 8, 1, 85, 85, 86, 86, 86, 86, 86, 86, 86, 86] 86 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 321 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054877 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054877 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054877/0.* 1: /scratch/stefan/7922901/working/building/REAL250005054877/1.* 2: /scratch/stefan/7922901/working/building/REAL250005054877/2.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054877 Building REAL250005054878 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054878' /scratch/stefan/7922901/working/building/REAL250005054878 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054878 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054878/0 /scratch/stefan/7922901/working/building/REAL250005054878 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1037 `/scratch/stefan/7922901/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCOC1CC1) `REAL250005054878.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054878 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCOC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 56, 80, 150, 164, 201, 201, 201, 201, 201, 201, 201, 201, 30, 56, 17, 6, 1, 1, 1, 1, 80, 80, 80, 150, 150, 164, 164, 201, 201, 30, 30, 17, 17, 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: 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: REAL250005054878 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCOC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 24, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 51, 66, 66, 68, 97, 140, 201, 201, 51, 51, 51, 24, 24, 13, 13, 4, 1, 68, 68, 97, 97, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054878 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054878 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054878/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054878 Building REAL250005054879 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054879' /scratch/stefan/7922901/working/building/REAL250005054879 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054879 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054879/0 /scratch/stefan/7922901/working/building/REAL250005054879 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1038 `/scratch/stefan/7922901/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCCCO) `REAL250005054879.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054879 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CCCCCO NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [65, 33, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 98, 98, 106, 131, 159, 201, 201, 65, 65, 65, 33, 33, 18, 18, 4, 1, 106, 106, 131, 131, 159, 159, 201, 201, 201, 201, 603] 603 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1481 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054879 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054879 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054879/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054879 Building REAL250005054880 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054880' /scratch/stefan/7922901/working/building/REAL250005054880 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054880 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054880/0 /scratch/stefan/7922901/working/building/REAL250005054880 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1039 `/scratch/stefan/7922901/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCO)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054880.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054880 none CC(CCO)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [38, 30, 38, 43, 43, 27, 30, 21, 27, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 43, 43, 43, 43, 129, 27, 27, 27, 21, 21, 15, 15, 4, 1] 129 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: 324 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054880 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054880 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054880/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054880 Building REAL250005054881 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054881' /scratch/stefan/7922901/working/building/REAL250005054881 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054881 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054881/0 /scratch/stefan/7922901/working/building/REAL250005054881 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1040 `/scratch/stefan/7922901/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)=CC1CC1) `REAL250005054881.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054881 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)=CC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'F', 'C.2', '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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 32, 60, 106, 145, 201, 201, 201, 201, 201, 201, 201, 201, 7, 32, 7, 7, 1, 1, 1, 1, 60, 60, 60, 106, 106, 145, 145, 201, 201, 7, 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: 765 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054881 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)=CC1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.2', 'F', 'C.2', '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: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 1, 15, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 32, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 67, 117, 117, 143, 143, 143, 201, 201, 67, 67, 67, 32, 32, 16, 16, 4, 1, 143, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 727 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054881 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054881 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054881/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054881 Building REAL250005054882 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054882' /scratch/stefan/7922901/working/building/REAL250005054882 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054882 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054882/0 /scratch/stefan/7922901/working/building/REAL250005054882 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1041 `/scratch/stefan/7922901/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CC(F)C1) `REAL250005054882.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054882 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CC(F)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 33, 67, 94, 201, 201, 201, 201, 201, 201, 201, 201, 6, 17, 1, 1, 1, 1, 1, 1, 33, 33, 33, 67, 67, 94, 94, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 717 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: REAL250005054882 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CC1CC(F)C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 5, 15, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 62, 122, 122, 131, 201, 201, 201, 201, 62, 62, 62, 32, 32, 22, 22, 4, 1, 131, 131, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 732 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054882 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054882 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054882/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054882 Building REAL250005054883 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054883' /scratch/stefan/7922901/working/building/REAL250005054883 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054883 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054883/0 /scratch/stefan/7922901/working/building/REAL250005054883 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1042 `/scratch/stefan/7922901/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H](O)CF) `REAL250005054883.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054883 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)[C@H](O)CF NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 7, 12, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [89, 36, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 89, 152, 152, 187, 187, 187, 201, 89, 89, 89, 36, 36, 19, 19, 4, 1, 561, 201, 201] 603 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 1343 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054883 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054883 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054883/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054883 Building REAL250005054884 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054884' /scratch/stefan/7922901/working/building/REAL250005054884 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054884 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054884/0 /scratch/stefan/7922901/working/building/REAL250005054884 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1043 `/scratch/stefan/7922901/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CCO)CC1) `REAL250005054884.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054884 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CCO)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 18, 26, 43, 43, 43, 49, 49, 49, 49, 49, 1, 3, 1, 1, 7, 14, 1, 1, 7, 7, 7, 18, 18, 26, 26, 43, 49, 7, 7, 14, 14, 42, 1, 1, 1, 1] 171 rigid atoms, others: [35, 36, 37, 38, 13, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 281 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054884 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(CCO)CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [33, 20, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 33, 49, 49, 49, 57, 57, 49, 49, 33, 33, 33, 20, 20, 13, 13, 4, 1, 57, 57, 57, 57, 171, 49, 49, 49, 49] 171 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 392 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054884 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054884 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054884/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054884 Building REAL250005054885 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054885' /scratch/stefan/7922901/working/building/REAL250005054885 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054885 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054885/0 /scratch/stefan/7922901/working/building/REAL250005054885 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1044 `/scratch/stefan/7922901/working/3D/1044' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(O)C(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054885.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054885 none CC(C)C(C)(O)C(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 243 conformations in input total number of sets (complete confs): 243 using faster count positions algorithm for large data unique positions, atoms: [81, 60, 81, 59, 60, 60, 43, 59, 23, 43, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 60, 60, 60, 180, 43, 43, 43, 23, 23, 14, 14, 4, 1] 243 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: 538 number of broken/clashed sets: 96 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054885 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054885 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054885/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054885 Building REAL250005054886 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054886' /scratch/stefan/7922901/working/building/REAL250005054886 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054886 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054886/0 /scratch/stefan/7922901/working/building/REAL250005054886 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1045 `/scratch/stefan/7922901/working/3D/1045' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(O)CCC1) `REAL250005054886.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054886 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(O)CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 363 conformations in input total number of sets (complete confs): 363 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 13, 39, 59, 112, 112, 112, 121, 121, 121, 121, 121, 1, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 39, 59, 59, 112, 121, 6, 1, 1, 1, 1, 1, 1] 363 rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 440 number of broken/clashed sets: 88 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054886 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C1(O)CCC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 363 conformations in input total number of sets (complete confs): 363 using faster count positions algorithm for large data unique positions, atoms: [72, 43, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 72, 112, 112, 121, 121, 121, 121, 72, 72, 72, 43, 43, 26, 26, 7, 1, 363, 121, 121, 121, 121, 121, 121] 363 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 804 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054886 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054886 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054886/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054886 Building REAL250005054887 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054887' /scratch/stefan/7922901/working/building/REAL250005054887 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054887 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054887/0 /scratch/stefan/7922901/working/building/REAL250005054887 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1046 `/scratch/stefan/7922901/working/3D/1046' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(O)C1CC1) `REAL250005054887.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054887 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(O)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 26, 53, 97, 137, 201, 201, 201, 201, 201, 201, 201, 201, 7, 26, 1, 7, 1, 1, 1, 53, 53, 53, 97, 97, 137, 137, 201, 201, 7, 21, 1, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 15, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 819 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054887 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(O)C1CC1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 36, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 70, 114, 114, 152, 152, 201, 201, 70, 70, 70, 36, 36, 22, 22, 4, 1, 152, 456, 201, 201, 201, 201, 201] 603 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1256 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054887 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054887 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054887/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054887 Building REAL250005054888 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054888' /scratch/stefan/7922901/working/building/REAL250005054888 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054888 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054888/0 /scratch/stefan/7922901/working/building/REAL250005054888 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1047 `/scratch/stefan/7922901/working/3D/1047' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=NN=C1) `REAL250005054888.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054888 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=NN=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 76, 116, 138, 201, 201, 201, 201, 201, 201, 201, 201, 8, 36, 1, 1, 1, 1, 1, 1, 76, 76, 76, 116, 116, 138, 138, 201, 201, 8, 8, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 757 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054888 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)CN1C=NN=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 24, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 72, 116, 116, 199, 201, 201, 201, 201, 72, 72, 72, 41, 41, 24, 24, 6, 1, 199, 199, 201, 201] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 29] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 810 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054888 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054888 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054888/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054888 Building REAL250005054889 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054889' /scratch/stefan/7922901/working/building/REAL250005054889 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054889 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054889/0 /scratch/stefan/7922901/working/building/REAL250005054889 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1048) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1048 `/scratch/stefan/7922901/working/3D/1048' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054889.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054889 none C=C(C)CC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 179, 181, 115, 85, 115, 52, 85, 32, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 179, 179, 85, 85, 85, 52, 52, 32, 32, 9, 1] 181 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054889 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054889 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054889/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054889 Building REAL250005054890 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054890' /scratch/stefan/7922901/working/building/REAL250005054890 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054890 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054890/0 /scratch/stefan/7922901/working/building/REAL250005054890 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1049) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1049 `/scratch/stefan/7922901/working/3D/1049' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)C#N) `REAL250005054890.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054890 none CN(CCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(C)(C)C#N NO_LONG_NAME dock atom types: ['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', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 17, 11, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 19, 21, 21, 21, 21, 21, 21, 19, 19, 19, 17, 17, 11, 11, 5, 1, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 91 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054890 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054890 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054890/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054890 Building REAL250005054891 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054891' /scratch/stefan/7922901/working/building/REAL250005054891 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054891 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054891/0 /scratch/stefan/7922901/working/building/REAL250005054891 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1050) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1050 `/scratch/stefan/7922901/working/3D/1050' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054891.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054891 none CCSCC(=O)N(C)CCNC(=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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 159, 107, 75, 67, 75, 40, 67, 24, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 109, 109, 67, 67, 67, 40, 40, 24, 24, 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: 787 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054891 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054891 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054891/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054891 Building REAL250005054892 mkdir: created directory `/scratch/stefan/7922901/working/building/REAL250005054892' /scratch/stefan/7922901/working/building/REAL250005054892 /scratch/stefan/7922901/working /scratch/stefan/7922901 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005054892 mkdir: created directory `0' /scratch/stefan/7922901/working/building/REAL250005054892/0 /scratch/stefan/7922901/working/building/REAL250005054892 /scratch/stefan/7922901/working /scratch/stefan/7922901 Protomer 0 (index: 1051) Found valid previously generated 3D confromation in /scratch/stefan/7922901/working/3D/1051 `/scratch/stefan/7922901/working/3D/1051' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)OCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1) `REAL250005054892.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005054892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7922901/working/building/REAL250005054892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005054892 none CC(=O)OCCC(=O)N(C)CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 12, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 88, 42, 36, 42, 26, 36, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 130, 130, 88, 88, 36, 36, 36, 26, 26, 17, 17, 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: 704 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7922901/working/building/REAL250005054892 /scratch/stefan/7922901/working /scratch/stefan/7922901 Finished preparing REAL250005054892 Recording results /scratch/stefan/7922901/working /scratch/stefan/7922901 Appending to /scratch/stefan/7922901/finished/xaaaaaq.* 0: /scratch/stefan/7922901/working/building/REAL250005054892/0.* Removing working files in /scratch/stefan/7922901/working/building/REAL250005054892 /scratch/stefan/7922901 Compressing combined databse files /scratch/stefan/7922901/finished/xaaaaaq.db2.gz /scratch/stefan/7922901/finished/xaaaaaq.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7922901/finished) ======================================================= Finalizing... removed `/scratch/stefan/7922901/working/3D/1052' removed directory: `/scratch/stefan/7922901/working/3D' `/scratch/stefan/7922901/working/protonate' -> `/scratch/stefan/7922901/archive' `/scratch/stefan/7922901/working/input-smiles.ism' -> `/scratch/stefan/7922901/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7922901/working/building' rmdir: removing directory, `/scratch/stefan/7922901/working' ls: No match. ls: No match.